projects / unres4.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
critical bug fix for ions langvin and fix pdb output for wham and cluster
[unres4.git] / source / unres / energy.F90
diff --git a/source/unres/energy.F90 b/source/unres/energy.F90
index 9ba038e..ec3ffd4 100644 (file)
--- a/source/unres/energy.F90
+++ b/source/unres/energy.F90
@@ -1,4 +1,4 @@
-             module energy
+            module energy
 !-----------------------------------------------------------------------------
       use io_units
       use names
 !-----------------------------------------------------------------------------
       use io_units
       use names
@@ -137,7 +137,7 @@
          gvdwc_peppho
 !------------------------------IONS GRADIENT
         real(kind=8),dimension(:,:),allocatable  ::  gradcatcat, &
          gvdwc_peppho
 !------------------------------IONS GRADIENT
         real(kind=8),dimension(:,:),allocatable  ::  gradcatcat, &
-          gradpepcat,gradpepcatx
+          gradpepcat,gradpepcatx,gradnuclcat,gradnuclcatx
 !      real(kind=8),dimension(:,:),allocatable :: gloc,gloc_x !(maxvar,2)
 
 
 !      real(kind=8),dimension(:,:),allocatable :: gloc,gloc_x !(maxvar,2)
 
 
@@ -236,7 +236,7 @@
 !      include 'COMMON.TIME1'
       real(kind=8) :: time00
 !el local variables
 !      include 'COMMON.TIME1'
       real(kind=8) :: time00
 !el local variables
-      integer :: n_corr,n_corr1,ierror
+      integer :: n_corr,n_corr1,ierror,imatupdate
       real(kind=8) :: etors,edihcnstr,etors_d,esccor,ehpb
       real(kind=8) :: evdw,evdw1,evdw2,evdw2_14,escloc,ees,eel_loc
       real(kind=8) :: eello_turn3,eello_turn4,estr,ebe,eliptran,etube, &
       real(kind=8) :: etors,edihcnstr,etors_d,esccor,ehpb
       real(kind=8) :: evdw,evdw1,evdw2,evdw2_14,escloc,ees,eel_loc
       real(kind=8) :: eello_turn3,eello_turn4,estr,ebe,eliptran,etube, &
@@ -247,7 +247,8 @@
                       ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,&
                       ecorr3_nucl
 ! energies for ions 
                       ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,&
                       ecorr3_nucl
 ! energies for ions 
-      real(kind=8) :: ecation_prot,ecationcation,ecations_prot_amber
+      real(kind=8) :: ecation_prot,ecationcation,ecations_prot_amber,&
+                      ecation_nucl
 ! energies for protein nucleic acid interaction
       real(kind=8) :: escbase,epepbase,escpho,epeppho
 
 ! energies for protein nucleic acid interaction
       real(kind=8) :: escbase,epepbase,escpho,epeppho
 
@@ -264,8 +265,9 @@
 
        integer ishield_listbuf(-1:nres), &
        shield_listbuf(maxcontsshi,-1:nres),k,j,i,iii,impishi,mojint,jjj
 
        integer ishield_listbuf(-1:nres), &
        shield_listbuf(maxcontsshi,-1:nres),k,j,i,iii,impishi,mojint,jjj
-
-
+!       print *,"I START ENERGY"
+       imatupdate=100
+!       if (mod(itime_mat,imatupdate).eq.0) call make_SCSC_inter_list
 !      real(kind=8),  dimension(:),allocatable::  fac_shieldbuf 
 !      real(kind=8), dimension(:,:,:),allocatable:: &
 !       grad_shield_locbuf,grad_shield_sidebuf
 !      real(kind=8),  dimension(:),allocatable::  fac_shieldbuf 
 !      real(kind=8), dimension(:,:,:),allocatable:: &
 !       grad_shield_locbuf,grad_shield_sidebuf
@@ -329,8 +331,10 @@
           weights_(41)=wcatcat
           weights_(42)=wcatprot
           weights_(46)=wscbase
           weights_(41)=wcatcat
           weights_(42)=wcatprot
           weights_(46)=wscbase
-          weights_(47)=wscpho
-          weights_(48)=wpeppho
+          weights_(47)=wpepbase
+          weights_(48)=wscpho
+          weights_(49)=wpeppho
+          weights_(50)=wcatnucl          
 !          wcatcat= weights(41)
 !          wcatprot=weights(42)
 
 !          wcatcat= weights(41)
 !          wcatprot=weights(42)
 
@@ -376,13 +380,36 @@
           wcatcat= weights(41)
           wcatprot=weights(42)
           wscbase=weights(46)
           wcatcat= weights(41)
           wcatprot=weights(42)
           wscbase=weights(46)
-          wscpho=weights(47)
-          wpeppho=weights(48)
+          wpepbase=weights(47)
+          wscpho=weights(48)
+          wpeppho=weights(49)
+          wcatnucl=weights(50)
+!      welpsb=weights(28)*fact(1)
+!
+!      wcorr_nucl= weights(37)*fact(1)
+!     wcorr3_nucl=weights(38)*fact(2)
+!     wtor_nucl=  weights(35)*fact(1)
+!     wtor_d_nucl=weights(36)*fact(2)
+
         endif
         time_Bcast=time_Bcast+MPI_Wtime()-time00
         time_Bcastw=time_Bcastw+MPI_Wtime()-time00
 !        call chainbuild_cart
       endif
         endif
         time_Bcast=time_Bcast+MPI_Wtime()-time00
         time_Bcastw=time_Bcastw+MPI_Wtime()-time00
 !        call chainbuild_cart
       endif
+!       print *,"itime_mat",itime_mat,imatupdate
+        if (nfgtasks.gt.1) then 
+        call MPI_Bcast(itime_mat,1,MPI_INT,king,FG_COMM,IERROR)
+        endif
+       if (nres_molec(1).gt.0) then
+       if (mod(itime_mat,imatupdate).eq.0) call make_SCp_inter_list
+!       write (iout,*) "after make_SCp_inter_list"
+       if (mod(itime_mat,imatupdate).eq.0) call make_SCSC_inter_list
+!       write (iout,*) "after make_SCSC_inter_list"
+
+       if (mod(itime_mat,imatupdate).eq.0) call make_pp_inter_list
+       endif
+!       write (iout,*) "after make_pp_inter_list"
+
 !      print *,'Processor',myrank,' calling etotal ipot=',ipot
 !      print *,'Processor',myrank,' nnt=',nnt,' nct=',nct
 #else
 !      print *,'Processor',myrank,' calling etotal ipot=',ipot
 !      print *,'Processor',myrank,' nnt=',nnt,' nct=',nct
 #else
@@ -819,10 +846,12 @@
       call epsb(evdwpsb,eelpsb)
       call esb(esbloc)
       call multibody_hb_nucl(ecorr_nucl,ecorr3_nucl,n_corr,n_corr1)
       call epsb(evdwpsb,eelpsb)
       call esb(esbloc)
       call multibody_hb_nucl(ecorr_nucl,ecorr3_nucl,n_corr,n_corr1)
+            call ecat_nucl(ecation_nucl)
       else
        etors_nucl=0.0d0
        estr_nucl=0.0d0
        ecorr3_nucl=0.0d0
       else
        etors_nucl=0.0d0
        estr_nucl=0.0d0
        ecorr3_nucl=0.0d0
+       ecorr_nucl=0.0d0
        ebe_nucl=0.0d0
        evdwsb=0.0d0
        eelsb=0.0d0
        ebe_nucl=0.0d0
        evdwsb=0.0d0
        eelsb=0.0d0
@@ -831,9 +860,12 @@
        eelpsb=0.0d0
        evdwpp=0.0d0
        eespp=0.0d0
        eelpsb=0.0d0
        evdwpp=0.0d0
        eespp=0.0d0
+       etors_d_nucl=0.0d0
+       ecation_nucl=0.0d0
       endif
 !      write(iout,*) ecorr_nucl,"ecorr_nucl",nres_molec(2)
 !      print *,"before ecatcat",wcatcat
       endif
 !      write(iout,*) ecorr_nucl,"ecorr_nucl",nres_molec(2)
 !      print *,"before ecatcat",wcatcat
+      if (nres_molec(5).gt.0) then
       if (nfgtasks.gt.1) then
       if (fg_rank.eq.0) then
       call ecatcat(ecationcation)
       if (nfgtasks.gt.1) then
       if (fg_rank.eq.0) then
       call ecatcat(ecationcation)
@@ -841,9 +873,16 @@
       else
       call ecatcat(ecationcation)
       endif
       else
       call ecatcat(ecationcation)
       endif
+      if (oldion.gt.0) then
       call ecat_prot(ecation_prot)
       call ecat_prot(ecation_prot)
-      call ecats_prot_amber(ecations_prot_amber)
-      if (nres_molec(2).gt.0) then
+      else
+      call ecats_prot_amber(ecation_prot)
+      endif
+      else
+      ecationcation=0.0d0
+      ecation_prot=0.0d0
+      endif
+      if ((nres_molec(2).gt.0).and.(nres_molec(1).gt.0)) then
       call eprot_sc_base(escbase)
       call epep_sc_base(epepbase)
       call eprot_sc_phosphate(escpho)
       call eprot_sc_base(escbase)
       call epep_sc_base(epepbase)
       call eprot_sc_phosphate(escpho)
@@ -855,7 +894,7 @@
       epeppho=0.0
       endif
 !      call ecatcat(ecationcation)
       epeppho=0.0
       endif
 !      call ecatcat(ecationcation)
-!      print *,"after ebend", ebe_nucl
+!      print *,"after ebend", wtor_nucl 
 #ifdef TIMING
       time_enecalc=time_enecalc+MPI_Wtime()-time00
 #endif
 #ifdef TIMING
       time_enecalc=time_enecalc+MPI_Wtime()-time00
 #endif
@@ -925,7 +964,8 @@
       energia(47)=epepbase
       energia(48)=escpho
       energia(49)=epeppho
       energia(47)=epepbase
       energia(48)=escpho
       energia(49)=epeppho
-      energia(50)=ecations_prot_amber
+!      energia(50)=ecations_prot_amber
+      energia(50)=ecation_nucl
       call sum_energy(energia,.true.)
       if (dyn_ss) call dyn_set_nss
 !      print *," Processor",myrank," left SUM_ENERGY"
       call sum_energy(energia,.true.)
       if (dyn_ss) call dyn_set_nss
 !      print *," Processor",myrank," left SUM_ENERGY"
@@ -968,7 +1008,8 @@
       real(kind=8) :: evdwpp,eespp,evdwpsb,eelpsb,evdwsb,eelsb,estr_nucl,&
                       ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,&
                       ecorr3_nucl
       real(kind=8) :: evdwpp,eespp,evdwpsb,eelpsb,evdwsb,eelsb,estr_nucl,&
                       ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,&
                       ecorr3_nucl
-      real(kind=8) :: ecation_prot,ecationcation,ecations_prot_amber
+      real(kind=8) :: ecation_prot,ecationcation,ecations_prot_amber,&
+                      ecation_nucl
       real(kind=8) :: escbase,epepbase,escpho,epeppho
       integer :: i
 #ifdef MPI
       real(kind=8) :: escbase,epepbase,escpho,epeppho
       integer :: i
 #ifdef MPI
@@ -1052,7 +1093,8 @@
       epepbase=energia(47)
       escpho=energia(48)
       epeppho=energia(49)
       epepbase=energia(47)
       escpho=energia(48)
       epeppho=energia(49)
-      ecations_prot_amber=energia(50)
+      ecation_nucl=energia(50)
+!      ecations_prot_amber=energia(50)
 
 !      energia(41)=ecation_prot
 !      energia(42)=ecationcation
 
 !      energia(41)=ecation_prot
 !      energia(42)=ecationcation
@@ -1071,7 +1113,7 @@
        +wvdwsb*evdwsb+welsb*eelsb+wsbloc*esbloc+wtor_nucl*etors_nucl&
        +wtor_d_nucl*etors_d_nucl+wcorr_nucl*ecorr_nucl+wcorr3_nucl*ecorr3_nucl&
        +wcatprot*ecation_prot+wcatcat*ecationcation+wscbase*escbase&
        +wvdwsb*evdwsb+welsb*eelsb+wsbloc*esbloc+wtor_nucl*etors_nucl&
        +wtor_d_nucl*etors_d_nucl+wcorr_nucl*ecorr_nucl+wcorr3_nucl*ecorr3_nucl&
        +wcatprot*ecation_prot+wcatcat*ecationcation+wscbase*escbase&
-       +wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho+ecations_prot_amber
+       +wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho+wcatnucl*ecation_nucl
 #else
       etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1) &
        +wang*ebe+wtor*etors+wscloc*escloc &
 #else
       etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1) &
        +wang*ebe+wtor*etors+wscloc*escloc &
@@ -1085,7 +1127,7 @@
        +wvdwsb*evdwsb+welsb*eelsb+wsbloc*esbloc+wtor_nucl*etors_nucl&
        +wtor_d_nucl*etors_d_nucl+wcorr_nucl*ecorr_nucl+wcorr3_nucl*ecorr3_nucl&
        +wcatprot*ecation_prot+wcatcat*ecationcation+wscbase*escbase&
        +wvdwsb*evdwsb+welsb*eelsb+wsbloc*esbloc+wtor_nucl*etors_nucl&
        +wtor_d_nucl*etors_d_nucl+wcorr_nucl*ecorr_nucl+wcorr3_nucl*ecorr3_nucl&
        +wcatprot*ecation_prot+wcatcat*ecationcation+wscbase*escbase&
-       +wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho+ecations_prot_amber
+       +wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho+wcatnucl*ecation_nucl
 #endif
       energia(0)=etot
 ! detecting NaNQ
 #endif
       energia(0)=etot
 ! detecting NaNQ
@@ -1193,7 +1235,12 @@
       wtor=weights(13)*fact(1)
       wtor_d=weights(14)*fact(2)
       wsccor=weights(21)*fact(1)
       wtor=weights(13)*fact(1)
       wtor_d=weights(14)*fact(2)
       wsccor=weights(21)*fact(1)
-
+      welpsb=weights(28)*fact(1)
+      wcorr_nucl= weights(37)*fact(1)
+      wcorr3_nucl=weights(38)*fact(2)
+      wtor_nucl=  weights(35)*fact(1)
+      wtor_d_nucl=weights(36)*fact(2)
+      wpepbase=weights(47)*fact(1)
       return
       end subroutine rescale_weights
 !-----------------------------------------------------------------------------
       return
       end subroutine rescale_weights
 !-----------------------------------------------------------------------------
@@ -1213,7 +1260,8 @@
       real(kind=8) :: evdwpp,eespp,evdwpsb,eelpsb,evdwsb,eelsb,estr_nucl,&
                       ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,&
                       ecorr3_nucl
       real(kind=8) :: evdwpp,eespp,evdwpsb,eelpsb,evdwsb,eelsb,estr_nucl,&
                       ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,&
                       ecorr3_nucl
-      real(kind=8) :: ecation_prot,ecationcation,ecations_prot_amber
+      real(kind=8) :: ecation_prot,ecationcation,ecations_prot_amber,&
+                      ecation_nucl
       real(kind=8) :: escbase,epepbase,escpho,epeppho
 
       etot=energia(0)
       real(kind=8) :: escbase,epepbase,escpho,epeppho
 
       etot=energia(0)
@@ -1267,7 +1315,8 @@
       epepbase=energia(47)
       escpho=energia(48)
       epeppho=energia(49)
       epepbase=energia(47)
       escpho=energia(48)
       epeppho=energia(49)
-      ecations_prot_amber=energia(50)
+      ecation_nucl=energia(50)
+!      ecations_prot_amber=energia(50)
 #ifdef SPLITELE
       write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp,&
         estr,wbond,ebe,wang,&
 #ifdef SPLITELE
       write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp,&
         estr,wbond,ebe,wang,&
@@ -1283,7 +1332,7 @@
         etors_d_nucl,wtor_d_nucl,ecorr_nucl,wcorr_nucl,&
         ecorr3_nucl,wcorr3_nucl,ecation_prot,wcatprot,ecationcation,wcatcat, &
         escbase,wscbase,epepbase,wpepbase,escpho,wscpho,epeppho,wpeppho,&
         etors_d_nucl,wtor_d_nucl,ecorr_nucl,wcorr_nucl,&
         ecorr3_nucl,wcorr3_nucl,ecation_prot,wcatprot,ecationcation,wcatcat, &
         escbase,wscbase,epepbase,wpepbase,escpho,wscpho,epeppho,wpeppho,&
-        ecations_prot_amber,etot
+        ecation_nucl,wcatnucl,etot
    10 format (/'Virtual-chain energies:'// &
        'EVDW=  ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ &
        'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ &
    10 format (/'Virtual-chain energies:'// &
        'EVDW=  ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ &
        'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ &
@@ -1330,6 +1379,7 @@
        'EPEPBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-base)'/ &
        'ESCPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(sc-prot nucl-phosphate)'/&
        'EPEPPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-phosphate)'/&
        'EPEPBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-base)'/ &
        'ESCPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(sc-prot nucl-phosphate)'/&
        'EPEPPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-phosphate)'/&
+       'ECATBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(cation nucl-base)'/&
        'ETOT=  ',1pE16.6,' (total)')
 #else
       write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,&
        'ETOT=  ',1pE16.6,' (total)')
 #else
       write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,&
@@ -1346,7 +1396,7 @@
         etors_d_nucl,wtor_d_nucl,ecorr_nucl,wcorr_nucl,&
         ecorr3_nucl,wcorr3_nucl,ecation_prot,wcatprot,ecationcation,wcatcat,  &
         escbase,wscbase,epepbase,wpepbase,escpho,wscpho,epeppho,wpeppho,&
         etors_d_nucl,wtor_d_nucl,ecorr_nucl,wcorr_nucl,&
         ecorr3_nucl,wcorr3_nucl,ecation_prot,wcatprot,ecationcation,wcatcat,  &
         escbase,wscbase,epepbase,wpepbase,escpho,wscpho,epeppho,wpeppho,&
-        ecations_prot_amber,etot
+        ecation_nucl,wcatnucl,etot
    10 format (/'Virtual-chain energies:'// &
        'EVDW=  ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ &
        'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ &
    10 format (/'Virtual-chain energies:'// &
        'EVDW=  ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ &
        'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ &
@@ -1392,6 +1442,7 @@
        'EPEPBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-base)'/ &
        'ESCPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(sc-prot nucl-phosphate)'/&
        'EPEPPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-phosphate)'/&
        'EPEPBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-base)'/ &
        'ESCPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(sc-prot nucl-phosphate)'/&
        'EPEPPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-phosphate)'/&
+       'ECATBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(cation nucl-base)'/&
        'ETOT=  ',1pE16.6,' (total)')
 #endif
       return
        'ETOT=  ',1pE16.6,' (total)')
 #endif
       return
@@ -1420,7 +1471,8 @@
       integer :: num_conti
 !el local variables
       integer :: i,itypi,iint,j,itypi1,itypj,k
       integer :: num_conti
 !el local variables
       integer :: i,itypi,iint,j,itypi1,itypj,k
-      real(kind=8) :: rij,rcut,fcont,fprimcont,rrij
+      real(kind=8) :: rij,rcut,fcont,fprimcont,rrij,sslipi,ssgradlipi,&
+       aa,bb,sslipj,ssgradlipj
       real(kind=8) :: evdw,xi,yi,zi,xj,yj,zj
       real(kind=8) :: eps0ij,fac,e1,e2,evdwij,sigij,r0ij
 
       real(kind=8) :: evdw,xi,yi,zi,xj,yj,zj
       real(kind=8) :: eps0ij,fac,e1,e2,evdwij,sigij,r0ij
 
@@ -1438,6 +1490,9 @@
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+
 ! Change 12/1/95
         num_conti=0
 !
 ! Change 12/1/95
         num_conti=0
 !
@@ -1452,6 +1507,15 @@
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
+            call to_box(xj,yj,zj)
+            call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+            aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            xj=boxshift(xj-xi,boxxsize)
+            yj=boxshift(yj-yi,boxysize)
+            zj=boxshift(zj-zi,boxzsize)
 ! Change 12/1/95 to calculate four-body interactions
             rij=xj*xj+yj*yj+zj*zj
             rrij=1.0D0/rij
 ! Change 12/1/95 to calculate four-body interactions
             rij=xj*xj+yj*yj+zj*zj
             rrij=1.0D0/rij
@@ -1584,7 +1648,8 @@
       logical :: scheck
 !el local variables
       integer :: i,iint,j,itypi,itypi1,k,itypj
       logical :: scheck
 !el local variables
       integer :: i,iint,j,itypi,itypi1,k,itypj
-      real(kind=8) :: rrij,xi,yi,zi,xj,yj,zj,fac_augm,e_augm,r_inv_ij
+      real(kind=8) :: rrij,xi,yi,zi,xj,yj,zj,fac_augm,e_augm,r_inv_ij, &
+         sslipi,ssgradlipi, sslipj,ssgradlipj, aa, bb
       real(kind=8) :: evdw,rij,r_shift_inv,fac,e1,e2,evdwij
 
 !     print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
       real(kind=8) :: evdw,rij,r_shift_inv,fac,e1,e2,evdwij
 
 !     print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
@@ -1596,6 +1661,9 @@
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+
 !
 ! Calculate SC interaction energy.
 !
 !
 ! Calculate SC interaction energy.
 !
@@ -1606,6 +1674,15 @@
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
+            call to_box(xj,yj,zj)
+            call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+            aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            xj=boxshift(xj-xi,boxxsize)
+            yj=boxshift(yj-yi,boxysize)
+            zj=boxshift(zj-zi,boxzsize)
             rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
             fac_augm=rrij**expon
             e_augm=augm(itypi,itypj)*fac_augm
             rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
             fac_augm=rrij**expon
             e_augm=augm(itypi,itypj)*fac_augm
@@ -1679,7 +1756,8 @@
       logical :: lprn
 !el local variables
       integer :: iint,itypi,itypi1,itypj
       logical :: lprn
 !el local variables
       integer :: iint,itypi,itypi1,itypj
-      real(kind=8) :: rrij,xi,yi,zi
+      real(kind=8) :: rrij,xi,yi,zi, sslipi,ssgradlipi, sslipj, &
+        ssgradlipj, aa, bb
       real(kind=8) :: evdw,fac,e1,e2,sigm,epsi
 
 !     print *,'Entering EBP nnt=',nnt,' nct=',nct,' expon=',expon
       real(kind=8) :: evdw,fac,e1,e2,sigm,epsi
 
 !     print *,'Entering EBP nnt=',nnt,' nct=',nct,' expon=',expon
@@ -1697,6 +1775,8 @@
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
@@ -1734,6 +1814,15 @@
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
+            call to_box(xj,yj,zj)
+            call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+            aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            xj=boxshift(xj-xi,boxxsize)
+            yj=boxshift(yj-yi,boxysize)
+            zj=boxshift(zj-zi,boxzsize)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
@@ -1806,7 +1895,7 @@
 !      include 'COMMON.SBRIDGE'
       logical :: lprn
 !el local variables
 !      include 'COMMON.SBRIDGE'
       logical :: lprn
 !el local variables
-      integer :: iint,itypi,itypi1,itypj,subchap
+      integer :: iint,itypi,itypi1,itypj,subchap,icont
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
       real(kind=8) :: evdw,sig0ij
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
       real(kind=8) :: evdw,sig0ij
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
@@ -1827,9 +1916,13 @@
       dCAVdOM1=0.0d0 
       dGCLdOM1=0.0d0 
       dPOLdOM1=0.0d0
       dCAVdOM1=0.0d0 
       dGCLdOM1=0.0d0 
       dPOLdOM1=0.0d0
-
-
-      do i=iatsc_s,iatsc_e
+!             write (iout,*) "RWA", g_listscsc_start,g_listscsc_end,i,j
+      if (nres_molec(1).eq.0) return
+      do icont=g_listscsc_start,g_listscsc_end
+      i=newcontlisti(icont)
+      j=newcontlistj(icont)
+!      write (iout,*) "RWA", g_listscsc_start,g_listscsc_end,i,j
+!      do i=iatsc_s,iatsc_e
 !C        print *,"I am in EVDW",i
         itypi=iabs(itype(i,1))
 !        if (i.ne.47) cycle
 !C        print *,"I am in EVDW",i
         itypi=iabs(itype(i,1))
 !        if (i.ne.47) cycle
@@ -1838,36 +1931,9 @@
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
-          xi=dmod(xi,boxxsize)
-          if (xi.lt.0) xi=xi+boxxsize
-          yi=dmod(yi,boxysize)
-          if (yi.lt.0) yi=yi+boxysize
-          zi=dmod(zi,boxzsize)
-          if (zi.lt.0) zi=zi+boxzsize
-
-       if ((zi.gt.bordlipbot)  &
-        .and.(zi.lt.bordliptop)) then
-!C the energy transfer exist
-        if (zi.lt.buflipbot) then
-!C what fraction I am in
-         fracinbuf=1.0d0-  &
-              ((zi-bordlipbot)/lipbufthick)
-!C lipbufthick is thickenes of lipid buffore
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
-        elseif (zi.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
-        else
-         sslipi=1.0d0
-         ssgradlipi=0.0
-        endif
-       else
-         sslipi=0.0d0
-         ssgradlipi=0.0
-       endif
-!       print *, sslipi,ssgradlipi
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
@@ -1878,8 +1944,8 @@
 !
 ! Calculate SC interaction energy.
 !
 !
 ! Calculate SC interaction energy.
 !
-        do iint=1,nint_gr(i)
-          do j=istart(i,iint),iend(i,iint)
+!        do iint=1,nint_gr(i)
+!          do j=istart(i,iint),iend(i,iint)
             IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
               call dyn_ssbond_ene(i,j,evdwij)
               evdw=evdw+evdwij
             IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
               call dyn_ssbond_ene(i,j,evdwij)
               evdw=evdw+evdwij
@@ -1887,7 +1953,7 @@
                               'evdw',i,j,evdwij,' ss'
 !              if (energy_dec) write (iout,*) &
 !                              'evdw',i,j,evdwij,' ss'
                               'evdw',i,j,evdwij,' ss'
 !              if (energy_dec) write (iout,*) &
 !                              'evdw',i,j,evdwij,' ss'
-             do k=j+1,iend(i,iint)
+             do k=j+1,nres
 !C search over all next residues
               if (dyn_ss_mask(k)) then
 !C check if they are cysteins
 !C search over all next residues
               if (dyn_ss_mask(k)) then
 !C check if they are cysteins
@@ -1941,73 +2007,16 @@
            xj=c(1,nres+j)
            yj=c(2,nres+j)
            zj=c(3,nres+j)
            xj=c(1,nres+j)
            yj=c(2,nres+j)
            zj=c(3,nres+j)
-          xj=dmod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=dmod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=dmod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-!          print *,"tu",xi,yi,zi,xj,yj,zj
-!          print *,"tu2",j,j+nres,c(1,j),c(1,j+nres)
-! this fragment set correct epsilon for lipid phase
-       if ((zj.gt.bordlipbot)  &
-       .and.(zj.lt.bordliptop)) then
-!C the energy transfer exist
-        if (zj.lt.buflipbot) then
-!C what fraction I am in
-         fracinbuf=1.0d0-     &
-             ((zj-bordlipbot)/lipbufthick)
-!C lipbufthick is thickenes of lipid buffore
-         sslipj=sscalelip(fracinbuf)
-         ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
-        elseif (zj.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
-         sslipj=sscalelip(fracinbuf)
-         ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
-        else
-         sslipj=1.0d0
-         ssgradlipj=0.0
-        endif
-       else
-         sslipj=0.0d0
-         ssgradlipj=0.0
-       endif
-      aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0   &
-       +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
-      bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0   &
-       +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
-!------------------------------------------------
-      dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-      xj_safe=xj
-      yj_safe=yj
-      zj_safe=zj
-      subchap=0
-      do xshift=-1,1
-      do yshift=-1,1
-      do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-       enddo
-       enddo
-       enddo
-       if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-       else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-       endif
+              call to_box(xj,yj,zj)
+              call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+!              write (iout,*) "KWA2", itypi,itypj
+              aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+               +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+              bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+               +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+              xj=boxshift(xj-xi,boxxsize)
+              yj=boxshift(yj-yi,boxysize)
+              zj=boxshift(zj-zi,boxzsize)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
@@ -2104,8 +2113,8 @@
 ! Calculate angular part of the gradient.
             call sc_grad
             ENDIF    ! dyn_ss            
 ! Calculate angular part of the gradient.
             call sc_grad
             ENDIF    ! dyn_ss            
-          enddo      ! j
-        enddo        ! iint
+!          enddo      ! j
+!        enddo        ! iint
       enddo          ! i
 !       print *,"ZALAMKA", evdw
 !      write (iout,*) "Number of loop steps in EGB:",ind
       enddo          ! i
 !       print *,"ZALAMKA", evdw
 !      write (iout,*) "Number of loop steps in EGB:",ind
@@ -2137,7 +2146,8 @@
       logical :: lprn
 !el local variables
       integer :: iint,itypi,itypi1,itypj
       logical :: lprn
 !el local variables
       integer :: iint,itypi,itypi1,itypj
-      real(kind=8) :: rrij,xi,yi,zi,r0ij,fac_augm,e_augm,fac,e1,e2,sigm
+      real(kind=8) :: rrij,xi,yi,zi,r0ij,fac_augm,e_augm,fac,e1,e2, &
+         sigm,sslipi,ssgradlipi, sslipj,ssgradlipj, aa, bb
       real(kind=8) :: evdw,sig0ij,sig,rij_shift,epsi
 
 !     print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
       real(kind=8) :: evdw,sig0ij,sig,rij_shift,epsi
 
 !     print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
@@ -2152,6 +2162,8 @@
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
@@ -2191,6 +2203,15 @@
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
+           call to_box(xj,yj,zj)
+           call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+           aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+            +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+           bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+            +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+           xj=boxshift(xj-xi,boxxsize)
+           yj=boxshift(yj-yi,boxysize)
+           zj=boxshift(zj-zi,boxzsize)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
@@ -2284,6 +2305,8 @@
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
+        call to_box(xi,yi,zi)
+
 !
 ! Calculate SC interaction energy.
 !
 !
 ! Calculate SC interaction energy.
 !
@@ -2293,9 +2316,9 @@
           do j=istart(i,iint),iend(i,iint)
             itypj=iabs(itype(j,1))
             if (itypj.eq.ntyp1) cycle
           do j=istart(i,iint),iend(i,iint)
             itypj=iabs(itype(j,1))
             if (itypj.eq.ntyp1) cycle
-            xj=c(1,nres+j)-xi
-            yj=c(2,nres+j)-yi
-            zj=c(3,nres+j)-zi
+            xj=boxshift(c(1,nres+j)-xi,boxxsize)
+            yj=boxshift(c(2,nres+j)-yi,boxysize)
+            zj=boxshift(c(3,nres+j)-zi,boxzsize)
             rij=xj*xj+yj*yj+zj*zj
 !           write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj
             r0ij=r0(itypi,itypj)
             rij=xj*xj+yj*yj+zj*zj
 !           write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj
             r0ij=r0(itypi,itypj)
@@ -2372,6 +2395,7 @@
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
+        call to_box(xmedi,ymedi,zmedi)
         num_conti=0
 !        write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
         do j=ielstart(i),ielend(i)
         num_conti=0
 !        write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
         do j=ielstart(i),ielend(i)
@@ -2388,6 +2412,10 @@
           xj=c(1,j)+0.5D0*dxj-xmedi
           yj=c(2,j)+0.5D0*dyj-ymedi
           zj=c(3,j)+0.5D0*dzj-zmedi
           xj=c(1,j)+0.5D0*dxj-xmedi
           yj=c(2,j)+0.5D0*dyj-ymedi
           zj=c(3,j)+0.5D0*dzj-zmedi
+          call to_box(xj,yj,zj)
+          xj=boxshift(xj-xmedi,boxxsize)
+          yj=boxshift(yj-ymedi,boxysize)
+          zj=boxshift(zj-zmedi,boxzsize)
           rij=xj*xj+yj*yj+zj*zj
           if (rij.lt.r0ijsq) then
             evdw1ij=0.25d0*(rij-r0ijsq)**2
           rij=xj*xj+yj*yj+zj*zj
           if (rij.lt.r0ijsq) then
             evdw1ij=0.25d0*(rij-r0ijsq)**2
@@ -2844,7 +2872,17 @@
 #endif
 #else
         if (i.gt. nnt+2 .and. i.lt.nct+2) then
 #endif
 #else
         if (i.gt. nnt+2 .and. i.lt.nct+2) then
+!         write(iout,*) "i,",molnum(i),nloctyp
+!         print *, "i,",molnum(i),i,itype(i-2,1)
+        if (molnum(i).eq.1) then
+          if (itype(i-2,1).eq.ntyp1) then
+           iti=nloctyp
+          else
           iti = itype2loc(itype(i-2,1))
           iti = itype2loc(itype(i-2,1))
+          endif
+        else
+          iti=nloctyp
+        endif
         else
           iti=nloctyp
         endif
         else
           iti=nloctyp
         endif
@@ -3020,7 +3058,7 @@
 !        if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
         if (i.gt. nnt+1 .and. i.lt.nct+1) then
           if (itype(i-1,1).eq.0) then
 !        if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
         if (i.gt. nnt+1 .and. i.lt.nct+1) then
           if (itype(i-1,1).eq.0) then
-           iti1=ntortyp+1
+           iti1=nloctyp
           elseif (itype(i-1,1).le.ntyp) then
             iti1 = itype2loc(itype(i-1,1))
           else
           elseif (itype(i-1,1).le.ntyp) then
             iti1 = itype2loc(itype(i-1,1))
           else
@@ -3384,7 +3422,7 @@
                                              0.0d0,1.0d0,0.0d0,&
                                              0.0d0,0.0d0,1.0d0/),shape(unmat)) 
 !el local variables
                                              0.0d0,1.0d0,0.0d0,&
                                              0.0d0,0.0d0,1.0d0/),shape(unmat)) 
 !el local variables
-      integer :: i,k,j
+      integer :: i,k,j,icont
       real(kind=8) :: ees,evdw1,eel_loc,eello_turn3,eello_turn4
       real(kind=8) :: fac,t_eelecij,fracinbuf
     
       real(kind=8) :: ees,evdw1,eel_loc,eello_turn3,eello_turn4
       real(kind=8) :: fac,t_eelecij,fracinbuf
     
@@ -3412,6 +3450,7 @@
       eel_loc=0.0d0 
       eello_turn3=0.0d0
       eello_turn4=0.0d0
       eel_loc=0.0d0 
       eello_turn3=0.0d0
       eello_turn4=0.0d0
+      if (nres_molec(1).eq.0) return
 !
 
       if (icheckgrad.eq.1) then
 !
 
       if (icheckgrad.eq.1) then
@@ -3496,36 +3535,9 @@
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
-          xmedi=dmod(xmedi,boxxsize)
-          if (xmedi.lt.0) xmedi=xmedi+boxxsize
-          ymedi=dmod(ymedi,boxysize)
-          if (ymedi.lt.0) ymedi=ymedi+boxysize
-          zmedi=dmod(zmedi,boxzsize)
-          if (zmedi.lt.0) zmedi=zmedi+boxzsize
+        call to_box(xmedi,ymedi,zmedi)
+        call lipid_layer(xmedi,ymedi,zmedi,sslipi,ssgradlipi)
         num_conti=0
         num_conti=0
-       if ((zmedi.gt.bordlipbot) &
-        .and.(zmedi.lt.bordliptop)) then
-!C the energy transfer exist
-        if (zmedi.lt.buflipbot) then
-!C what fraction I am in
-         fracinbuf=1.0d0- &
-               ((zmedi-bordlipbot)/lipbufthick)
-!C lipbufthick is thickenes of lipid buffore
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
-        elseif (zmedi.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-zmedi)/lipbufthick)
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
-        else
-         sslipi=1.0d0
-         ssgradlipi=0.0
-        endif
-       else
-         sslipi=0.0d0
-         ssgradlipi=0.0
-       endif 
-!       print *,i,sslipi,ssgradlipi
        call eelecij(i,i+2,ees,evdw1,eel_loc)
         if (wturn3.gt.0.0d0) call eturn3(i,eello_turn3)
         num_cont_hb(i)=num_conti
        call eelecij(i,i+2,ees,evdw1,eel_loc)
         if (wturn3.gt.0.0d0) call eturn3(i,eello_turn3)
         num_cont_hb(i)=num_conti
@@ -3544,39 +3556,12 @@
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
-          xmedi=dmod(xmedi,boxxsize)
-          if (xmedi.lt.0) xmedi=xmedi+boxxsize
-          ymedi=dmod(ymedi,boxysize)
-          if (ymedi.lt.0) ymedi=ymedi+boxysize
-          zmedi=dmod(zmedi,boxzsize)
-          if (zmedi.lt.0) zmedi=zmedi+boxzsize
-       if ((zmedi.gt.bordlipbot)  &
-       .and.(zmedi.lt.bordliptop)) then
-!C the energy transfer exist
-        if (zmedi.lt.buflipbot) then
-!C what fraction I am in
-         fracinbuf=1.0d0- &
-             ((zmedi-bordlipbot)/lipbufthick)
-!C lipbufthick is thickenes of lipid buffore
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
-        elseif (zmedi.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-zmedi)/lipbufthick)
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
-        else
-         sslipi=1.0d0
-         ssgradlipi=0.0
-        endif
-       else
-         sslipi=0.0d0
-         ssgradlipi=0.0
-       endif
-
+        call to_box(xmedi,ymedi,zmedi)
+        call lipid_layer(xmedi,ymedi,zmedi,sslipi,ssgradlipi)
         num_conti=num_cont_hb(i)
         call eelecij(i,i+3,ees,evdw1,eel_loc)
         if (wturn4.gt.0.0d0 .and. itype(i+2,1).ne.ntyp1) &
         num_conti=num_cont_hb(i)
         call eelecij(i,i+3,ees,evdw1,eel_loc)
         if (wturn4.gt.0.0d0 .and. itype(i+2,1).ne.ntyp1) &
-         call eturn4(i,eello_turn4)
+        call eturn4(i,eello_turn4)
 !        print *,"before",i,i+3, gshieldc_t4(2,i+3),gshieldc_t4(2,i)
         num_cont_hb(i)=num_conti
       enddo   ! i
 !        print *,"before",i,i+3, gshieldc_t4(2,i+3),gshieldc_t4(2,i)
         num_cont_hb(i)=num_conti
       enddo   ! i
@@ -3584,7 +3569,11 @@
 ! Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3
 !
 !      print *,"iatel_s,iatel_e,",iatel_s,iatel_e
 ! Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3
 !
 !      print *,"iatel_s,iatel_e,",iatel_s,iatel_e
-      do i=iatel_s,iatel_e
+!      do i=iatel_s,iatel_e
+! JPRDLC
+       do icont=g_listpp_start,g_listpp_end
+        i=newcontlistppi(icont)
+        j=newcontlistppj(icont)
         if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
         dxi=dc(1,i)
         dyi=dc(2,i)
         if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
         dxi=dc(1,i)
         dyi=dc(2,i)
@@ -3595,42 +3584,16 @@
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
-          xmedi=dmod(xmedi,boxxsize)
-          if (xmedi.lt.0) xmedi=xmedi+boxxsize
-          ymedi=dmod(ymedi,boxysize)
-          if (ymedi.lt.0) ymedi=ymedi+boxysize
-          zmedi=dmod(zmedi,boxzsize)
-          if (zmedi.lt.0) zmedi=zmedi+boxzsize
-       if ((zmedi.gt.bordlipbot)  &
-        .and.(zmedi.lt.bordliptop)) then
-!C the energy transfer exist
-        if (zmedi.lt.buflipbot) then
-!C what fraction I am in
-         fracinbuf=1.0d0- &
-             ((zmedi-bordlipbot)/lipbufthick)
-!C lipbufthick is thickenes of lipid buffore
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
-        elseif (zmedi.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-zmedi)/lipbufthick)
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
-        else
-         sslipi=1.0d0
-         ssgradlipi=0.0
-        endif
-       else
-         sslipi=0.0d0
-         ssgradlipi=0.0
-       endif
+        call to_box(xmedi,ymedi,zmedi)
+        call lipid_layer(xmedi,ymedi,zmedi,sslipi,ssgradlipi)
 
 !        write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
         num_conti=num_cont_hb(i)
 
 !        write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
         num_conti=num_cont_hb(i)
-        do j=ielstart(i),ielend(i)
+!        do j=ielstart(i),ielend(i)
 !          write (iout,*) i,j,itype(i,1),itype(j,1)
           if (itype(j,1).eq.ntyp1.or. itype(j+1,1).eq.ntyp1) cycle
           call eelecij(i,j,ees,evdw1,eel_loc)
 !          write (iout,*) i,j,itype(i,1),itype(j,1)
           if (itype(j,1).eq.ntyp1.or. itype(j+1,1).eq.ntyp1) cycle
           call eelecij(i,j,ees,evdw1,eel_loc)
-        enddo ! j
+!        enddo ! j
         num_cont_hb(i)=num_conti
       enddo   ! i
 !      write (iout,*) "Number of loop steps in EELEC:",ind
         num_cont_hb(i)=num_conti
       enddo   ! i
 !      write (iout,*) "Number of loop steps in EELEC:",ind
@@ -3697,6 +3660,7 @@
 !el local variables
       integer :: k,i,j,iteli,itelj,kkk,l,kkll,m,isubchap
       real(kind=8) :: ael6i,rrmij,rmij,r0ij,fcont,fprimcont,ees0tmp
 !el local variables
       integer :: k,i,j,iteli,itelj,kkk,l,kkll,m,isubchap
       real(kind=8) :: ael6i,rrmij,rmij,r0ij,fcont,fprimcont,ees0tmp
+      real(kind=8) ::  faclipij2, faclipij
       real(kind=8) :: ees,evdw1,eel_loc,aaa,bbb,ael3i
       real(kind=8) :: dxj,dyj,dzj,dx_normj,dy_normj,dz_normj,xj,yj,zj,&
                   rij,r3ij,r6ij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,&
       real(kind=8) :: ees,evdw1,eel_loc,aaa,bbb,ael3i
       real(kind=8) :: dxj,dyj,dzj,dx_normj,dy_normj,dz_normj,xj,yj,zj,&
                   rij,r3ij,r6ij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,&
@@ -3732,67 +3696,14 @@
           xj=c(1,j)+0.5D0*dxj
           yj=c(2,j)+0.5D0*dyj
           zj=c(3,j)+0.5D0*dzj
           xj=c(1,j)+0.5D0*dxj
           yj=c(2,j)+0.5D0*dyj
           zj=c(3,j)+0.5D0*dzj
-          xj=mod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=mod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=mod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-       if ((zj.gt.bordlipbot)  &
-       .and.(zj.lt.bordliptop)) then
-!C the energy transfer exist
-        if (zj.lt.buflipbot) then
-!C what fraction I am in
-         fracinbuf=1.0d0-     &
-             ((zj-bordlipbot)/lipbufthick)
-!C lipbufthick is thickenes of lipid buffore
-         sslipj=sscalelip(fracinbuf)
-         ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
-        elseif (zj.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
-         sslipj=sscalelip(fracinbuf)
-         ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
-        else
-         sslipj=1.0d0
-         ssgradlipj=0.0
-        endif
-       else
-         sslipj=0.0d0
-         ssgradlipj=0.0
-       endif
 
 
-      isubchap=0
-      dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
-      xj_safe=xj
-      yj_safe=yj
-      zj_safe=zj
-      do xshift=-1,1
-      do yshift=-1,1
-      do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            isubchap=1
-          endif
-       enddo
-       enddo
-       enddo
-       if (isubchap.eq.1) then
-!C          print *,i,j
-          xj=xj_temp-xmedi
-          yj=yj_temp-ymedi
-          zj=zj_temp-zmedi
-       else
-          xj=xj_safe-xmedi
-          yj=yj_safe-ymedi
-          zj=zj_safe-zmedi
-       endif
+          call to_box(xj,yj,zj)
+          call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+          faclipij=(sslipi+sslipj)/2.0d0*lipscale+1.0d0
+          faclipij2=(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0
+          xj=boxshift(xj-xmedi,boxxsize)
+          yj=boxshift(yj-ymedi,boxysize)
+          zj=boxshift(zj-zmedi,boxzsize)
 
           rij=xj*xj+yj*yj+zj*zj
           rrmij=1.0D0/rij
 
           rij=xj*xj+yj*yj+zj*zj
           rrmij=1.0D0/rij
@@ -3804,7 +3715,7 @@
 !             sss_ele_grad=0.0d0
 !            print *,sss_ele_cut,sss_ele_grad,&
 !            (rij),r_cut_ele,rlamb_ele
 !             sss_ele_grad=0.0d0
 !            print *,sss_ele_cut,sss_ele_grad,&
 !            (rij),r_cut_ele,rlamb_ele
-!            if (sss_ele_cut.le.0.0) go to 128
+            if (sss_ele_cut.le.0.0) go to 128
 
           rmij=1.0D0/rij
           r3ij=rrmij*rmij
 
           rmij=1.0D0/rij
           r3ij=rrmij*rmij
@@ -4020,11 +3931,11 @@
 !grad            enddo
 !grad          enddo
 ! 9/28/08 AL Gradient compotents will be summed only at the end
 !grad            enddo
 !grad          enddo
 ! 9/28/08 AL Gradient compotents will be summed only at the end
-          ggg(1)=facvdw*xj &
+          ggg(1)=facvdw*xj+sss_ele_grad*rmij*evdwij*xj &
            *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
            *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
-          ggg(2)=facvdw*yj &
+          ggg(2)=facvdw*yj+sss_ele_grad*rmij*evdwij*yj &
            *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
            *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
-          ggg(3)=facvdw*zj &
+          ggg(3)=facvdw*zj+sss_ele_grad*rmij*evdwij*zj &
            *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
           do k=1,3
            *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
           do k=1,3
@@ -4353,7 +4264,9 @@
           +a32*gmuij1(3)&
           +a33*gmuij1(4))&
          *fac_shield(i)*fac_shield(j)&
           +a32*gmuij1(3)&
           +a33*gmuij1(4))&
          *fac_shield(i)*fac_shield(j)&
-                    *sss_ele_cut
+                    *sss_ele_cut     &
+         *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
 
 !c         write(iout,*) "derivative over thatai"
 !c         write(iout,*) a22*gmuij1(1), a23*gmuij1(2) ,a32*gmuij1(3),
 
 !c         write(iout,*) "derivative over thatai"
 !c         write(iout,*) a22*gmuij1(1), a23*gmuij1(2) ,a32*gmuij1(3),
@@ -4371,7 +4284,8 @@
          gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+&
            geel_loc_ij*wel_loc&
          *fac_shield(i)*fac_shield(j)&
          gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+&
            geel_loc_ij*wel_loc&
          *fac_shield(i)*fac_shield(j)&
-                    *sss_ele_cut
+                    *sss_ele_cut &
+         *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
 
 !c  Derivative over j residue
 
 
 !c  Derivative over j residue
@@ -4386,7 +4300,8 @@
         gloc(nphi+j,icg)=gloc(nphi+j,icg)+&
            geel_loc_ji*wel_loc&
          *fac_shield(i)*fac_shield(j)&
         gloc(nphi+j,icg)=gloc(nphi+j,icg)+&
            geel_loc_ji*wel_loc&
          *fac_shield(i)*fac_shield(j)&
-                    *sss_ele_cut
+                    *sss_ele_cut &
+         *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
 
          geel_loc_ji=&
 
 
          geel_loc_ji=&
@@ -4400,7 +4315,9 @@
          gloc(nphi+j-1,icg)=gloc(nphi+j-1,icg)+&
            geel_loc_ji*wel_loc&
          *fac_shield(i)*fac_shield(j)&
          gloc(nphi+j-1,icg)=gloc(nphi+j-1,icg)+&
            geel_loc_ji*wel_loc&
          *fac_shield(i)*fac_shield(j)&
-                    *sss_ele_cut
+                    *sss_ele_cut &
+         *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
 #endif
 
 !          write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
 #endif
 
 !          write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
@@ -4599,10 +4516,12 @@
                 ees0p(num_conti,i)=0.5D0*fac3*(ees0pij+ees0mij) &
                      *sss_ele_cut &
                      *fac_shield(i)*fac_shield(j)
                 ees0p(num_conti,i)=0.5D0*fac3*(ees0pij+ees0mij) &
                      *sss_ele_cut &
                      *fac_shield(i)*fac_shield(j)
+!                     *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
                 ees0m(num_conti,i)=0.5D0*fac3*(ees0pij-ees0mij) &
                      *sss_ele_cut &
                      *fac_shield(i)*fac_shield(j)
 
                 ees0m(num_conti,i)=0.5D0*fac3*(ees0pij-ees0mij) &
                      *sss_ele_cut &
                      *fac_shield(i)*fac_shield(j)
+!                     *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
 ! Diagnostics. Comment out or remove after debugging!
 !               ees0p(num_conti,i)=0.5D0*fac3*ees0pij
 
 ! Diagnostics. Comment out or remove after debugging!
 !               ees0p(num_conti,i)=0.5D0*fac3*ees0pij
@@ -4681,28 +4600,36 @@
                   gacontp_hb1(k,num_conti,i)= & !ghalfp+
                     (ecosap*(dc_norm(k,j)-cosa*dc_norm(k,i)) &
                    + ecosbp*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1) &
                   gacontp_hb1(k,num_conti,i)= & !ghalfp+
                     (ecosap*(dc_norm(k,j)-cosa*dc_norm(k,i)) &
                    + ecosbp*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1) &
-                     *sss_ele_cut*fac_shield(i)*fac_shield(j)
+                     *sss_ele_cut*fac_shield(i)*fac_shield(j) ! &
+!                     *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
 
                   gacontp_hb2(k,num_conti,i)= & !ghalfp+
                     (ecosap*(dc_norm(k,i)-cosa*dc_norm(k,j)) &
                    + ecosgp*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)&
 
                   gacontp_hb2(k,num_conti,i)= & !ghalfp+
                     (ecosap*(dc_norm(k,i)-cosa*dc_norm(k,j)) &
                    + ecosgp*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)&
-                     *sss_ele_cut*fac_shield(i)*fac_shield(j)
+                     *sss_ele_cut*fac_shield(i)*fac_shield(j)!   &
+!                     *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
 
                   gacontp_hb3(k,num_conti,i)=gggp(k) &
                      *sss_ele_cut*fac_shield(i)*fac_shield(j)
 
                   gacontp_hb3(k,num_conti,i)=gggp(k) &
                      *sss_ele_cut*fac_shield(i)*fac_shield(j)
+!                     *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
                   gacontm_hb1(k,num_conti,i)= & !ghalfm+
                     (ecosam*(dc_norm(k,j)-cosa*dc_norm(k,i)) &
                    + ecosbm*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1) &
                      *sss_ele_cut*fac_shield(i)*fac_shield(j)
 
                   gacontm_hb1(k,num_conti,i)= & !ghalfm+
                     (ecosam*(dc_norm(k,j)-cosa*dc_norm(k,i)) &
                    + ecosbm*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1) &
                      *sss_ele_cut*fac_shield(i)*fac_shield(j)
+!                     *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
                   gacontm_hb2(k,num_conti,i)= & !ghalfm+
                     (ecosam*(dc_norm(k,i)-cosa*dc_norm(k,j)) &
                    + ecosgm*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1) &
                      *sss_ele_cut*fac_shield(i)*fac_shield(j)
 
                   gacontm_hb2(k,num_conti,i)= & !ghalfm+
                     (ecosam*(dc_norm(k,i)-cosa*dc_norm(k,j)) &
                    + ecosgm*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1) &
                      *sss_ele_cut*fac_shield(i)*fac_shield(j)
+!                     *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
                   gacontm_hb3(k,num_conti,i)=gggm(k) &
                      *sss_ele_cut*fac_shield(i)*fac_shield(j)
 
                   gacontm_hb3(k,num_conti,i)=gggm(k) &
                      *sss_ele_cut*fac_shield(i)*fac_shield(j)
+!                     *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
                 enddo
 ! Diagnostics. Comment out or remove after debugging!
 
                 enddo
 ! Diagnostics. Comment out or remove after debugging!
@@ -4775,36 +4702,14 @@
 !el         num_conti,j1,j2
 !el local variables
       integer :: i,j,l,k,ilist,iresshield
 !el         num_conti,j1,j2
 !el local variables
       integer :: i,j,l,k,ilist,iresshield
-      real(kind=8) :: eello_turn3,zj,fracinbuf,eello_t3, rlocshield
-
+      real(kind=8) :: eello_turn3,zj,fracinbuf,eello_t3, rlocshield,xj,yj
+      xj=0.0d0
+      yj=0.0d0
       j=i+2
 !      write (iout,*) "eturn3",i,j,j1,j2
           zj=(c(3,j)+c(3,j+1))/2.0d0
       j=i+2
 !      write (iout,*) "eturn3",i,j,j1,j2
           zj=(c(3,j)+c(3,j+1))/2.0d0
-          zj=mod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-          if ((zj.lt.0)) write (*,*) "CHUJ"
-       if ((zj.gt.bordlipbot)  &
-        .and.(zj.lt.bordliptop)) then
-!C the energy transfer exist
-        if (zj.lt.buflipbot) then
-!C what fraction I am in
-         fracinbuf=1.0d0-     &
-             ((zj-bordlipbot)/lipbufthick)
-!C lipbufthick is thickenes of lipid buffore
-         sslipj=sscalelip(fracinbuf)
-         ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
-        elseif (zj.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
-         sslipj=sscalelip(fracinbuf)
-         ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
-        else
-         sslipj=1.0d0
-         ssgradlipj=0.0
-        endif
-       else
-         sslipj=0.0d0
-         ssgradlipj=0.0
-       endif
+            call to_box(xj,yj,zj)
+            call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
 
       a_temp(1,1)=a22
       a_temp(1,2)=a23
 
       a_temp(1,1)=a22
       a_temp(1,2)=a23
@@ -4849,10 +4754,15 @@
 !C Derivatives in theta
         gloc(nphi+i,icg)=gloc(nphi+i,icg) &
        +0.5d0*(gpizda1(1,1)+gpizda1(2,2))*wturn3&
 !C Derivatives in theta
         gloc(nphi+i,icg)=gloc(nphi+i,icg) &
        +0.5d0*(gpizda1(1,1)+gpizda1(2,2))*wturn3&
-        *fac_shield(i)*fac_shield(j)
+        *fac_shield(i)*fac_shield(j) &
+        *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
         gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)&
        +0.5d0*(gpizda2(1,1)+gpizda2(2,2))*wturn3&
         gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)&
        +0.5d0*(gpizda2(1,1)+gpizda2(2,2))*wturn3&
-        *fac_shield(i)*fac_shield(j)
+        *fac_shield(i)*fac_shield(j) &
+        *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
+
 !C#endif
 
 
 !C#endif
 
 
@@ -5013,8 +4923,9 @@
 !el local variables
       integer :: i,j,iti1,iti2,iti3,l,k,ilist,iresshield
       real(kind=8) :: eello_turn4,s1,s2,s3,zj,fracinbuf,eello_t4,&
 !el local variables
       integer :: i,j,iti1,iti2,iti3,l,k,ilist,iresshield
       real(kind=8) :: eello_turn4,s1,s2,s3,zj,fracinbuf,eello_t4,&
-         rlocshield,gs23,gs32,gsE13,gs13,gs21,gsE31,gsEE1,gsEE2,gsEE3
-      
+         rlocshield,gs23,gs32,gsE13,gs13,gs21,gsE31,gsEE1,gsEE2,gsEE3,xj,yj
+      xj=0.0d0
+      yj=0.0d0 
       j=i+3
 !      if (j.ne.20) return
 !      print *,i,j,gshieldc_t4(2,j),gshieldc_t4(2,j+1)
       j=i+3
 !      if (j.ne.20) return
 !      print *,i,j,gshieldc_t4(2,j),gshieldc_t4(2,j+1)
@@ -5032,30 +4943,9 @@
 !d        call checkint_turn4(i,a_temp,eello_turn4_num)
 !        write (iout,*) "eturn4 i",i," j",j," j1",j1," j2",j2
           zj=(c(3,j)+c(3,j+1))/2.0d0
 !d        call checkint_turn4(i,a_temp,eello_turn4_num)
 !        write (iout,*) "eturn4 i",i," j",j," j1",j1," j2",j2
           zj=(c(3,j)+c(3,j+1))/2.0d0
-          zj=mod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-       if ((zj.gt.bordlipbot)  &
-        .and.(zj.lt.bordliptop)) then
-!C the energy transfer exist
-        if (zj.lt.buflipbot) then
-!C what fraction I am in
-         fracinbuf=1.0d0-     &
-             ((zj-bordlipbot)/lipbufthick)
-!C lipbufthick is thickenes of lipid buffore
-         sslipj=sscalelip(fracinbuf)
-         ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
-        elseif (zj.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
-         sslipj=sscalelip(fracinbuf)
-         ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
-        else
-         sslipj=1.0d0
-         ssgradlipj=0.0
-        endif
-       else
-         sslipj=0.0d0
-         ssgradlipj=0.0
-       endif
+            call to_box(xj,yj,zj)
+            call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+
 
         a_temp(1,1)=a22
         a_temp(1,2)=a23
 
         a_temp(1,1)=a22
         a_temp(1,2)=a23
@@ -5174,14 +5064,19 @@
 #ifdef NEWCORR
         gloc(nphi+i,icg)=gloc(nphi+i,icg)&
                        -(gs13+gsE13+gsEE1)*wturn4&
 #ifdef NEWCORR
         gloc(nphi+i,icg)=gloc(nphi+i,icg)&
                        -(gs13+gsE13+gsEE1)*wturn4&
-       *fac_shield(i)*fac_shield(j)
+       *fac_shield(i)*fac_shield(j) &
+       *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
         gloc(nphi+i+1,icg)= gloc(nphi+i+1,icg)&
                          -(gs23+gs21+gsEE2)*wturn4&
         gloc(nphi+i+1,icg)= gloc(nphi+i+1,icg)&
                          -(gs23+gs21+gsEE2)*wturn4&
-       *fac_shield(i)*fac_shield(j)
+       *fac_shield(i)*fac_shield(j)&
+       *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
         gloc(nphi+i+2,icg)= gloc(nphi+i+2,icg)&
                          -(gs32+gsE31+gsEE3)*wturn4&
 
         gloc(nphi+i+2,icg)= gloc(nphi+i+2,icg)&
                          -(gs32+gsE31+gsEE3)*wturn4&
-       *fac_shield(i)*fac_shield(j)
+       *fac_shield(i)*fac_shield(j)&
+       *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
 
 !c         gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)-
 !c     &   gs2
 
 !c         gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)-
 !c     &   gs2
@@ -5403,6 +5298,7 @@
         xi=0.5D0*(c(1,i)+c(1,i+1))
         yi=0.5D0*(c(2,i)+c(2,i+1))
         zi=0.5D0*(c(3,i)+c(3,i+1))
         xi=0.5D0*(c(1,i)+c(1,i+1))
         yi=0.5D0*(c(2,i)+c(2,i+1))
         zi=0.5D0*(c(3,i)+c(3,i+1))
+          call to_box(xi,yi,zi)
 
         do iint=1,nscp_gr(i)
 
 
         do iint=1,nscp_gr(i)
 
@@ -5417,6 +5313,10 @@
           xj=c(1,j)-xi
           yj=c(2,j)-yi
           zj=c(3,j)-zi
           xj=c(1,j)-xi
           yj=c(2,j)-yi
           zj=c(3,j)-zi
+          call to_box(xj,yj,zj)
+          xj=boxshift(xj-xi,boxxsize)
+          yj=boxshift(yj-yi,boxysize)
+          zj=boxshift(zj-zi,boxzsize)
           rij=xj*xj+yj*yj+zj*zj
           r0ij=r0_scp
           r0ijsq=r0ij*r0ij
           rij=xj*xj+yj*yj+zj*zj
           r0ij=r0_scp
           r0ijsq=r0ij*r0ij
@@ -5490,7 +5390,7 @@
 !      include 'COMMON.CONTROL'
       real(kind=8),dimension(3) :: ggg
 !el local variables
 !      include 'COMMON.CONTROL'
       real(kind=8),dimension(3) :: ggg
 !el local variables
-      integer :: i,iint,j,k,iteli,itypj,subchap
+      integer :: i,iint,j,k,iteli,itypj,subchap,icont
       real(kind=8) :: evdw2,evdw2_14,xi,yi,zi,xj,yj,zj,rrij,fac,&
                    e1,e2,evdwij,rij
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
       real(kind=8) :: evdw2,evdw2_14,xi,yi,zi,xj,yj,zj,rrij,fac,&
                    e1,e2,evdwij,rij
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
@@ -5501,22 +5401,21 @@
       evdw2_14=0.0d0
 !d    print '(a)','Enter ESCP'
 !d    write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
       evdw2_14=0.0d0
 !d    print '(a)','Enter ESCP'
 !d    write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
-      do i=iatscp_s,iatscp_e
+!      do i=iatscp_s,iatscp_e
+      if (nres_molec(1).eq.0) return
+       do icont=g_listscp_start,g_listscp_end
+        i=newcontlistscpi(icont)
+        j=newcontlistscpj(icont)
         if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
         iteli=itel(i)
         xi=0.5D0*(c(1,i)+c(1,i+1))
         yi=0.5D0*(c(2,i)+c(2,i+1))
         zi=0.5D0*(c(3,i)+c(3,i+1))
         if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
         iteli=itel(i)
         xi=0.5D0*(c(1,i)+c(1,i+1))
         yi=0.5D0*(c(2,i)+c(2,i+1))
         zi=0.5D0*(c(3,i)+c(3,i+1))
-          xi=mod(xi,boxxsize)
-          if (xi.lt.0) xi=xi+boxxsize
-          yi=mod(yi,boxysize)
-          if (yi.lt.0) yi=yi+boxysize
-          zi=mod(zi,boxzsize)
-          if (zi.lt.0) zi=zi+boxzsize
+        call to_box(xi,yi,zi)
 
 
-        do iint=1,nscp_gr(i)
+!        do iint=1,nscp_gr(i)
 
 
-        do j=iscpstart(i,iint),iscpend(i,iint)
+!        do j=iscpstart(i,iint),iscpend(i,iint)
           itypj=iabs(itype(j,1))
           if (itypj.eq.ntyp1) cycle
 ! Uncomment following three lines for SC-p interactions
           itypj=iabs(itype(j,1))
           if (itypj.eq.ntyp1) cycle
 ! Uncomment following three lines for SC-p interactions
@@ -5530,43 +5429,11 @@
           xj=c(1,j)
           yj=c(2,j)
           zj=c(3,j)
           xj=c(1,j)
           yj=c(2,j)
           zj=c(3,j)
-          xj=mod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=mod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=mod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-      dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-      xj_safe=xj
-      yj_safe=yj
-      zj_safe=zj
-      subchap=0
-      do xshift=-1,1
-      do yshift=-1,1
-      do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-       enddo
-       enddo
-       enddo
-       if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-       else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-       endif
+
+          call to_box(xj,yj,zj)
+          xj=boxshift(xj-xi,boxxsize)
+          yj=boxshift(yj-yi,boxysize)
+          zj=boxshift(zj-zi,boxzsize)
 
           rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
           rij=dsqrt(1.0d0/rrij)
 
           rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
           rij=dsqrt(1.0d0/rrij)
@@ -5628,9 +5495,9 @@
             gvdwc_scpp(k,i)=gvdwc_scpp(k,i)-ggg(k)
             gvdwc_scp(k,j)=gvdwc_scp(k,j)+ggg(k)
           enddo
             gvdwc_scpp(k,i)=gvdwc_scpp(k,i)-ggg(k)
             gvdwc_scp(k,j)=gvdwc_scp(k,j)+ggg(k)
           enddo
-        enddo
+!        enddo
 
 
-        enddo ! iint
+!        enddo ! iint
       enddo ! i
       do i=1,nct
         do j=1,3
       enddo ! i
       do i=1,nct
         do j=1,3
@@ -5697,7 +5564,7 @@
         iabs(itype(jjj,1)).eq.1) then
           call ssbond_ene(iii,jjj,eij)
           ehpb=ehpb+2*eij
         iabs(itype(jjj,1)).eq.1) then
           call ssbond_ene(iii,jjj,eij)
           ehpb=ehpb+2*eij
-!d          write (iout,*) "eij",eij
+!          write (iout,*) "eij",eij,iii,jjj
          endif
         else if (ii.gt.nres .and. jj.gt.nres) then
 !c Restraints from contact prediction
          endif
         else if (ii.gt.nres .and. jj.gt.nres) then
 !c Restraints from contact prediction
@@ -5826,6 +5693,8 @@
       xi=c(1,nres+i)
       yi=c(2,nres+i)
       zi=c(3,nres+i)
       xi=c(1,nres+i)
       yi=c(2,nres+i)
       zi=c(3,nres+i)
+          call to_box(xi,yi,zi)
+
       dxi=dc_norm(1,nres+i)
       dyi=dc_norm(2,nres+i)
       dzi=dc_norm(3,nres+i)
       dxi=dc_norm(1,nres+i)
       dyi=dc_norm(2,nres+i)
       dzi=dc_norm(3,nres+i)
@@ -5834,9 +5703,13 @@
       itypj=iabs(itype(j,1))
 !      dscj_inv=dsc_inv(itypj)
       dscj_inv=vbld_inv(nres+j)
       itypj=iabs(itype(j,1))
 !      dscj_inv=dsc_inv(itypj)
       dscj_inv=vbld_inv(nres+j)
-      xj=c(1,nres+j)-xi
-      yj=c(2,nres+j)-yi
-      zj=c(3,nres+j)-zi
+      xj=c(1,nres+j)
+      yj=c(2,nres+j)
+      zj=c(3,nres+j)
+          call to_box(xj,yj,zj)
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)
       dxj=dc_norm(1,nres+j)
       dyj=dc_norm(2,nres+j)
       dzj=dc_norm(3,nres+j)
       dxj=dc_norm(1,nres+j)
       dyj=dc_norm(2,nres+j)
       dzj=dc_norm(3,nres+j)
@@ -5861,9 +5734,9 @@
       eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2) &
         +akct*deltad*deltat12 &
         +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi+ebr
       eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2) &
         +akct*deltad*deltat12 &
         +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi+ebr
-!      write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth,
-!     &  " akct",akct," deltad",deltad," deltat",deltat1,deltat2,
-!     &  " deltat12",deltat12," eij",eij 
+!      write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth, &
+!       " akct",akct," deltad",deltad," deltat",deltat1,deltat2, &
+!       " deltat12",deltat12," eij",eij 
       ed=2*akcm*deltad+akct*deltat12
       pom1=akct*deltad
       pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi
       ed=2*akcm*deltad+akct*deltat12
       pom1=akct*deltad
       pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi
@@ -6921,6 +6794,8 @@
 !     &   dscp1,dscp2,sumene
 !        sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
         escloc = escloc + sumene
 !     &   dscp1,dscp2,sumene
 !        sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
         escloc = escloc + sumene
+       if (energy_dec) write (2,*) "i",i," itype",itype(i,1)," it",it, &
+        " escloc",sumene,escloc,it,itype(i,1)
 !        write (2,*) "i",i," escloc",sumene,escloc,it,itype(i,1)
 !     & ,zz,xx,yy
 !#define DEBUG
 !        write (2,*) "i",i," escloc",sumene,escloc,it,itype(i,1)
 !     & ,zz,xx,yy
 !#define DEBUG
@@ -11293,7 +11168,7 @@
                      wscbase*gvdwc_scbase(j,i)+ &
                      wpepbase*gvdwc_pepbase(j,i)+&
                      wscpho*gvdwc_scpho(j,i)+   &
                      wscbase*gvdwc_scbase(j,i)+ &
                      wpepbase*gvdwc_pepbase(j,i)+&
                      wscpho*gvdwc_scpho(j,i)+   &
-                     wpeppho*gvdwc_peppho(j,i)
+                     wpeppho*gvdwc_peppho(j,i)+wcatnucl*gradnuclcat(j,i)
 
        
 
 
        
 
@@ -11331,7 +11206,7 @@
                      wscbase*gvdwc_scbase(j,i)+ &
                      wpepbase*gvdwc_pepbase(j,i)+&
                      wscpho*gvdwc_scpho(j,i)+&
                      wscbase*gvdwc_scbase(j,i)+ &
                      wpepbase*gvdwc_pepbase(j,i)+&
                      wscpho*gvdwc_scpho(j,i)+&
-                     wpeppho*gvdwc_peppho(j,i)
+                     wpeppho*gvdwc_peppho(j,i)+wcatnucl*gradnuclcat(j,i)
 
 
         enddo
 
 
         enddo
@@ -11572,7 +11447,7 @@
                      +wbond_nucl*gradb_nucl(j,i) &
                      +0.5d0*(wvdwpp_nucl*gvdwpp_nucl(j,i)+welpp*gelpp(j,i)&
                      +wvdwpsb*gvdwpsb1(j,i))&
                      +wbond_nucl*gradb_nucl(j,i) &
                      +0.5d0*(wvdwpp_nucl*gvdwpp_nucl(j,i)+welpp*gelpp(j,i)&
                      +wvdwpsb*gvdwpsb1(j,i))&
-                     +wsbloc*gsbloc(j,i)
+                     +wsbloc*gsbloc(j,i)+wcatnucl*gradnuclcat(j,i)
 
 
 
 
 
 
@@ -11599,7 +11474,7 @@
                        +wcatprot* gradpepcatx(j,i)&
                        +wscbase*gvdwx_scbase(j,i) &
                        +wpepbase*gvdwx_pepbase(j,i)&
                        +wcatprot* gradpepcatx(j,i)&
                        +wscbase*gvdwx_scbase(j,i) &
                        +wpepbase*gvdwx_pepbase(j,i)&
-                       +wscpho*gvdwx_scpho(j,i)
+                       +wscpho*gvdwx_scpho(j,i)+wcatnucl*gradnuclcatx(j,i)
 !              if (i.eq.3) print *,"tu?", wscpho,gvdwx_scpho(j,i)
 
         enddo
 !              if (i.eq.3) print *,"tu?", wscpho,gvdwx_scpho(j,i)
 
         enddo
@@ -11648,7 +11523,7 @@
       enddo
 #endif
 !#undef DEBUG
       enddo
 #endif
 !#undef DEBUG
-        do i=1,nres
+        do i=0,nres
          do j=1,3
           gloc_scbuf(j,i)=gloc_sc(j,i,icg)
          enddo
          do j=1,3
           gloc_scbuf(j,i)=gloc_sc(j,i,icg)
          enddo
@@ -11664,14 +11539,14 @@
         call MPI_Reduce(glocbuf(1),gloc(1,icg),4*nres,&
           MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
         time_reduce=time_reduce+MPI_Wtime()-time00
         call MPI_Reduce(glocbuf(1),gloc(1,icg),4*nres,&
           MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
         time_reduce=time_reduce+MPI_Wtime()-time00
-        call MPI_Reduce(gloc_scbuf(1,1),gloc_sc(1,1,icg),3*nres,&
+        call MPI_Reduce(gloc_scbuf(1,0),gloc_sc(1,0,icg),3*nres+3,&
           MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
         time_reduce=time_reduce+MPI_Wtime()-time00
 !#define DEBUG
 !          print *,"gradbuf",gradbufc(1,1),gradc(1,1,icg)
 #ifdef DEBUG
       write (iout,*) "gloc_sc after reduce"
           MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
         time_reduce=time_reduce+MPI_Wtime()-time00
 !#define DEBUG
 !          print *,"gradbuf",gradbufc(1,1),gradc(1,1,icg)
 #ifdef DEBUG
       write (iout,*) "gloc_sc after reduce"
-      do i=1,nres
+      do i=0,nres
        do j=1,1
         write (iout,*) i,j,gloc_sc(j,i,icg)
        enddo
        do j=1,1
         write (iout,*) i,j,gloc_sc(j,i,icg)
        enddo
@@ -11873,15 +11748,8 @@
       end subroutine sc_grad
 
       subroutine sc_grad_cat
       end subroutine sc_grad
 
       subroutine sc_grad_cat
-!      implicit real*8 (a-h,o-z)
       use calc_data
       use calc_data
-!      include 'DIMENSIONS'
-!      include 'COMMON.CHAIN'
-!      include 'COMMON.DERIV'
-!      include 'COMMON.CALC'
-!      include 'COMMON.IOUNITS'
       real(kind=8), dimension(3) :: dcosom1,dcosom2
       real(kind=8), dimension(3) :: dcosom1,dcosom2
-!      print *,"wchodze"
       eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1 &
           +dCAVdOM1+ dGCLdOM1+ dPOLdOM1
       eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2 &
       eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1 &
           +dCAVdOM1+ dGCLdOM1+ dPOLdOM1
       eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2 &
@@ -11895,11 +11763,6 @@
 !      eom2=0.0d0
 !      eom12=evdwij*eps1_om12
 ! end diagnostics
 !      eom2=0.0d0
 !      eom12=evdwij*eps1_om12
 ! end diagnostics
-!      write (iout,*) "eps2der",eps2der," eps3der",eps3der,&
-!       " sigder",sigder
-!      write (iout,*) "eps1_om12",eps1_om12," eps2rt_om12",eps2rt_om12
-!      write (iout,*) "eom1",eom1," eom2",eom2," eom12",eom12
-!C      print *,sss_ele_cut,'in sc_grad'
 
       do k=1,3
         dcosom1(k)=rij*(dc_norm(k,nres+i)-om1*erij(k))
 
       do k=1,3
         dcosom1(k)=rij*(dc_norm(k,nres+i)-om1*erij(k))
@@ -11907,18 +11770,18 @@
       enddo
       do k=1,3
         gg(k)=(gg(k)+eom1*dcosom1(k)+eom2*dcosom2(k))
       enddo
       do k=1,3
         gg(k)=(gg(k)+eom1*dcosom1(k)+eom2*dcosom2(k))
-!C      print *,'gg',k,gg(k)
+!      print *,'gg',k,gg(k)
        enddo
 !       print *,i,j,gg_lipi(3),gg_lipj(3),sss_ele_cut
 !      write (iout,*) "gg",(gg(k),k=1,3)
       do k=1,3
        enddo
 !       print *,i,j,gg_lipi(3),gg_lipj(3),sss_ele_cut
 !      write (iout,*) "gg",(gg(k),k=1,3)
       do k=1,3
-        gvdwx(k,i)=gvdwx(k,i)-gg(k) +gg_lipi(k)&
+        gradpepcatx(k,i)=gradpepcatx(k,i)-gg(k) &
                   +(eom12*(dc_norm(k,j)-om12*dc_norm(k,nres+i)) &
                   +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
 
                   +(eom12*(dc_norm(k,j)-om12*dc_norm(k,nres+i)) &
                   +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
 
-        gvdwx(k,j)=gvdwx(k,j)+gg(k)+gg_lipj(k)&
-                  +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,j)) &
-                  +eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv   
+!        gradpepcatx(k,j)=gradpepcatx(k,j)+gg(k) &
+!                  +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,j)) &
+!                  +eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv   
 
 !        write (iout,*)(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
 !                 +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
 
 !        write (iout,*)(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
 !                 +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
@@ -11928,17 +11791,44 @@
 ! 
 ! Calculate the components of the gradient in DC and X
 !
 ! 
 ! Calculate the components of the gradient in DC and X
 !
-!grad      do k=i,j-1
-!grad        do l=1,3
-!grad          gvdwc(l,k)=gvdwc(l,k)+gg(l)
-!grad        enddo
-!grad      enddo
       do l=1,3
       do l=1,3
-        gvdwc(l,i)=gvdwc(l,i)-gg(l)
-        gvdwc(l,j)=gvdwc(l,j)+gg(l)
+        gradpepcat(l,i)=gradpepcat(l,i)-gg(l)
+        gradpepcat(l,j)=gradpepcat(l,j)+gg(l)
       enddo
       end subroutine sc_grad_cat
 
       enddo
       end subroutine sc_grad_cat
 
+      subroutine sc_grad_cat_pep
+      use calc_data
+      real(kind=8), dimension(3) :: dcosom1,dcosom2
+      eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1 &
+          +dCAVdOM1+ dGCLdOM1+ dPOLdOM1
+      eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2 &
+          +dCAVdOM2+ dGCLdOM2+ dPOLdOM2
+
+      eom12=evdwij*eps1_om12+eps2der*eps2rt_om12 &
+           -2.0D0*alf12*eps3der+sigder*sigsq_om12&
+           +dCAVdOM12+ dGCLdOM12
+! diagnostics only
+!      eom1=0.0d0
+!      eom2=0.0d0
+!      eom12=evdwij*eps1_om12
+! end diagnostics
+
+      do k=1,3
+        dcosom1(k) = rij * (dc_norm(k,i) - om1 * erij(k))
+        dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
+        gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
+        gvdwc_pepbase(k,i)= gvdwc_pepbase(k,i) +0.5*(- gg(k))   &
+                 + (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i)))&
+                 *dsci_inv*2.0 &
+                 - (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
+        gvdwc_pepbase(k,i+1)= gvdwc_pepbase(k,i+1) +0.5*(- gg(k))   &
+                 - (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i))) &
+                 *dsci_inv*2.0 &
+                 + (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
+        gradpepcat(k,j)=gradpepcat(k,j)+gg(k)
+      enddo
+      end subroutine sc_grad_cat_pep
 
 #ifdef CRYST_THETA
 !-----------------------------------------------------------------------------
 
 #ifdef CRYST_THETA
 !-----------------------------------------------------------------------------
@@ -12613,7 +12503,7 @@
 !      call intcartderiv
 !      call checkintcartgrad
       call zerograd
 !      call intcartderiv
 !      call checkintcartgrad
       call zerograd
-      aincr=1.0D-4
+      aincr=1.0D-5
       write(iout,*) 'Calling CHECK_ECARTINT.'
       nf=0
       icall=0
       write(iout,*) 'Calling CHECK_ECARTINT.'
       nf=0
       icall=0
@@ -12636,6 +12526,12 @@
           do j=1,3
             grad_s(j,i)=gcart(j,i)
             grad_s(j+3,i)=gxcart(j,i)
           do j=1,3
             grad_s(j,i)=gcart(j,i)
             grad_s(j+3,i)=gxcart(j,i)
+        write(iout,*) "before movement analytical gradient"
+        do i=1,nres
+          write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3),&
+          (gxcart(j,i),j=1,3)
+        enddo
+
           enddo
         enddo
       else
           enddo
         enddo
       else
@@ -12840,7 +12736,7 @@
 !      call intcartderiv
 !      call checkintcartgrad
       call zerograd
 !      call intcartderiv
 !      call checkintcartgrad
       call zerograd
-      aincr=1.0D-7
+      aincr=1.0D-6
       write(iout,*) 'Calling CHECK_ECARTINT.',aincr
       nf=0
       icall=0
       write(iout,*) 'Calling CHECK_ECARTINT.',aincr
       nf=0
       icall=0
@@ -12860,12 +12756,15 @@
         do i=1,nres
           do j=1,3
             grad_s(j,i)=gcart(j,i)
         do i=1,nres
           do j=1,3
             grad_s(j,i)=gcart(j,i)
-!              if (i.eq.21) print *,"PRZEKAZANIE",gcart(j,i)
-
-!            if (i.le.2) print *,"tu?!",gcart(j,i),grad_s(j,i),gxcart(j,i)
             grad_s(j+3,i)=gxcart(j,i)
           enddo
         enddo
             grad_s(j+3,i)=gxcart(j,i)
           enddo
         enddo
+        write(iout,*) "before movement analytical gradient"
+        do i=1,nres
+          write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3),&
+          (gxcart(j,i),j=1,3)
+        enddo
+
       else
 !- split gradient check
         call zerograd
       else
 !- split gradient check
         call zerograd
@@ -13316,7 +13215,8 @@
 !el local variables
       integer :: i,iint,j,k,itypi,itypi1,itypj
       real(kind=8) :: xi,yi,zi,xj,yj,zj,rij,sss,rrij,fac,eps0ij
 !el local variables
       integer :: i,iint,j,k,itypi,itypi1,itypj
       real(kind=8) :: xi,yi,zi,xj,yj,zj,rij,sss,rrij,fac,eps0ij
-      real(kind=8) :: e1,e2,evdwij,evdw
+      real(kind=8) :: e1,e2,evdwij,evdw,sslipi,ssgradlipi,&
+                      sslipj,ssgradlipj,aa,bb
 !      write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
       evdw=0.0D0
       do i=iatsc_s,iatsc_e
 !      write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
       evdw=0.0D0
       do i=iatsc_s,iatsc_e
@@ -13326,6 +13226,8 @@
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
 !
 ! Calculate SC interaction energy.
 !
 !
 ! Calculate SC interaction energy.
 !
@@ -13338,6 +13240,15 @@
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
+            call to_box(xj,yj,zj)
+            call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+            aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            xj=boxshift(xj-xi,boxxsize)
+            yj=boxshift(yj-yi,boxysize)
+            zj=boxshift(zj-zi,boxzsize)
             rij=xj*xj+yj*yj+zj*zj
             sss=sscale(dsqrt(rij)/sigma(itypi,itypj))
             if (sss.lt.1.0d0) then
             rij=xj*xj+yj*yj+zj*zj
             sss=sscale(dsqrt(rij)/sigma(itypi,itypj))
             if (sss.lt.1.0d0) then
@@ -13406,7 +13317,8 @@
 !el local variables
       integer :: i,iint,j,k,itypi,itypi1,itypj,num_conti
       real(kind=8) :: xi,yi,zi,xj,yj,zj,rij,sss,rrij,fac,eps0ij
 !el local variables
       integer :: i,iint,j,k,itypi,itypi1,itypj,num_conti
       real(kind=8) :: xi,yi,zi,xj,yj,zj,rij,sss,rrij,fac,eps0ij
-      real(kind=8) :: e1,e2,evdwij,evdw
+      real(kind=8) :: e1,e2,evdwij,evdw,sslipi,ssgradlipi,&
+                      sslipj,ssgradlipj
 !      write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
       evdw=0.0D0
       do i=iatsc_s,iatsc_e
 !      write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
       evdw=0.0D0
       do i=iatsc_s,iatsc_e
@@ -13416,6 +13328,8 @@
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
 ! Change 12/1/95
         num_conti=0
 !
 ! Change 12/1/95
         num_conti=0
 !
@@ -13506,6 +13420,8 @@
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
+          call to_box(xi,yi,zi)
+
 !
 ! Calculate SC interaction energy.
 !
 !
 ! Calculate SC interaction energy.
 !
@@ -13516,6 +13432,11 @@
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
+          call to_box(xj,yj,zj)
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)
+
             rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
             fac_augm=rrij**expon
             e_augm=augm(itypi,itypj)*fac_augm
             rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
             fac_augm=rrij**expon
             e_augm=augm(itypi,itypj)*fac_augm
@@ -13583,7 +13504,8 @@
 !el local variables
       integer :: i,iint,j,k,itypi,itypi1,itypj
       real(kind=8) :: rrij,r_inv_ij,xj,yj,zj,xi,yi,zi,fac,evdw,&
 !el local variables
       integer :: i,iint,j,k,itypi,itypi1,itypj
       real(kind=8) :: rrij,r_inv_ij,xj,yj,zj,xi,yi,zi,fac,evdw,&
-                   fac_augm,e_augm,rij,sss,r_shift_inv,e1,e2,evdwij
+                   fac_augm,e_augm,rij,sss,r_shift_inv,e1,e2,evdwij,&
+                   sslipi,ssgradlipi,sslipj,ssgradlipj,aa,bb
 !     print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
       evdw=0.0D0
       do i=iatsc_s,iatsc_e
 !     print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
       evdw=0.0D0
       do i=iatsc_s,iatsc_e
@@ -13593,6 +13515,8 @@
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
 !
 ! Calculate SC interaction energy.
 !
 !
 ! Calculate SC interaction energy.
 !
@@ -13603,6 +13527,15 @@
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
+            call to_box(xj,yj,zj)
+            call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+            aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            xj=boxshift(xj-xi,boxxsize)
+            yj=boxshift(yj-yi,boxysize)
+            zj=boxshift(zj-zi,boxzsize)
             rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
             fac_augm=rrij**expon
             e_augm=augm(itypi,itypj)*fac_augm
             rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
             fac_augm=rrij**expon
             e_augm=augm(itypi,itypj)*fac_augm
@@ -13650,12 +13583,11 @@
       return
       end subroutine eljk_short
 !-----------------------------------------------------------------------------
       return
       end subroutine eljk_short
 !-----------------------------------------------------------------------------
-      subroutine ebp_long(evdw)
-!
+       subroutine ebp_long(evdw)
 ! This subroutine calculates the interaction energy of nonbonded side chains
 ! assuming the Berne-Pechukas potential of interaction.
 !
 ! This subroutine calculates the interaction energy of nonbonded side chains
 ! assuming the Berne-Pechukas potential of interaction.
 !
-      use calc_data
+       use calc_data
 !      implicit real*8 (a-h,o-z)
 !      include 'DIMENSIONS'
 !      include 'COMMON.GEO'
 !      implicit real*8 (a-h,o-z)
 !      include 'DIMENSIONS'
 !      include 'COMMON.GEO'
@@ -13667,178 +13599,201 @@
 !      include 'COMMON.INTERACT'
 !      include 'COMMON.IOUNITS'
 !      include 'COMMON.CALC'
 !      include 'COMMON.INTERACT'
 !      include 'COMMON.IOUNITS'
 !      include 'COMMON.CALC'
-      use comm_srutu
+       use comm_srutu
 !el      integer :: icall
 !el      common /srutu/ icall
 !     double precision rrsave(maxdim)
 !el      integer :: icall
 !el      common /srutu/ icall
 !     double precision rrsave(maxdim)
-      logical :: lprn
+        logical :: lprn
 !el local variables
 !el local variables
-      integer :: iint,itypi,itypi1,itypj
-      real(kind=8) :: rrij,xi,yi,zi,fac
-      real(kind=8) :: sss,e1,e2,evdw,sigm,epsi
-      evdw=0.0D0
+        integer :: iint,itypi,itypi1,itypj
+        real(kind=8) :: rrij,xi,yi,zi,fac,sslipi,ssgradlipi,&
+                        sslipj,ssgradlipj,aa,bb
+        real(kind=8) :: sss,e1,e2,evdw,sigm,epsi
+        evdw=0.0D0
 !     print *,'Entering EBP nnt=',nnt,' nct=',nct,' expon=',expon
 !     print *,'Entering EBP nnt=',nnt,' nct=',nct,' expon=',expon
-      evdw=0.0D0
+        evdw=0.0D0
 !     if (icall.eq.0) then
 !       lprn=.true.
 !     else
 !     if (icall.eq.0) then
 !       lprn=.true.
 !     else
-        lprn=.false.
+      lprn=.false.
 !     endif
 !el      ind=0
       do i=iatsc_s,iatsc_e
 !     endif
 !el      ind=0
       do i=iatsc_s,iatsc_e
-        itypi=itype(i,1)
-        if (itypi.eq.ntyp1) cycle
-        itypi1=itype(i+1,1)
-        xi=c(1,nres+i)
-        yi=c(2,nres+i)
-        zi=c(3,nres+i)
-        dxi=dc_norm(1,nres+i)
-        dyi=dc_norm(2,nres+i)
-        dzi=dc_norm(3,nres+i)
-!        dsci_inv=dsc_inv(itypi)
-        dsci_inv=vbld_inv(i+nres)
-!
-! Calculate SC interaction energy.
-!
-        do iint=1,nint_gr(i)
-          do j=istart(i,iint),iend(i,iint)
+      itypi=itype(i,1)
+      if (itypi.eq.ntyp1) cycle
+      itypi1=itype(i+1,1)
+      xi=c(1,nres+i)
+      yi=c(2,nres+i)
+      zi=c(3,nres+i)
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+      dxi=dc_norm(1,nres+i)
+      dyi=dc_norm(2,nres+i)
+      dzi=dc_norm(3,nres+i)
+!        dsci_inv=dsc_inv(itypi)
+      dsci_inv=vbld_inv(i+nres)
+!
+! Calculate SC interaction energy.
+!
+      do iint=1,nint_gr(i)
+      do j=istart(i,iint),iend(i,iint)
 !el            ind=ind+1
 !el            ind=ind+1
-            itypj=itype(j,1)
-            if (itypj.eq.ntyp1) cycle
+      itypj=itype(j,1)
+      if (itypj.eq.ntyp1) cycle
 !            dscj_inv=dsc_inv(itypj)
 !            dscj_inv=dsc_inv(itypj)
-            dscj_inv=vbld_inv(j+nres)
-            chi1=chi(itypi,itypj)
-            chi2=chi(itypj,itypi)
-            chi12=chi1*chi2
-            chip1=chip(itypi)
-            chip2=chip(itypj)
-            chip12=chip1*chip2
-            alf1=alp(itypi)
-            alf2=alp(itypj)
-            alf12=0.5D0*(alf1+alf2)
-            xj=c(1,nres+j)-xi
-            yj=c(2,nres+j)-yi
-            zj=c(3,nres+j)-zi
-            dxj=dc_norm(1,nres+j)
-            dyj=dc_norm(2,nres+j)
-            dzj=dc_norm(3,nres+j)
-            rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
-            rij=dsqrt(rrij)
-            sss=sscale(1.0d0/(rij*sigmaii(itypi,itypj)))
-
-            if (sss.lt.1.0d0) then
-
-! Calculate the angle-dependent terms of energy & contributions to derivatives.
-              call sc_angular
-! Calculate whole angle-dependent part of epsilon and contributions
-! to its derivatives
-              fac=(rrij*sigsq)**expon2
-              e1=fac*fac*aa_aq(itypi,itypj)
-              e2=fac*bb_aq(itypi,itypj)
-              evdwij=eps1*eps2rt*eps3rt*(e1+e2)
-              eps2der=evdwij*eps3rt
-              eps3der=evdwij*eps2rt
-              evdwij=evdwij*eps2rt*eps3rt
-              evdw=evdw+evdwij*(1.0d0-sss)
-              if (lprn) then
-              sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0)
-              epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj)
-!d              write (iout,'(2(a3,i3,2x),15(0pf7.3))')
-!d     &          restyp(itypi,1),i,restyp(itypj,1),j,
-!d     &          epsi,sigm,chi1,chi2,chip1,chip2,
-!d     &          eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq),
-!d     &          om1,om2,om12,1.0D0/dsqrt(rrij),
-!d     &          evdwij
-              endif
-! Calculate gradient components.
-              e1=e1*eps1*eps2rt**2*eps3rt**2
-              fac=-expon*(e1+evdwij)
-              sigder=fac/sigsq
-              fac=rrij*fac
-! Calculate radial part of the gradient
-              gg(1)=xj*fac
-              gg(2)=yj*fac
-              gg(3)=zj*fac
-! Calculate the angular part of the gradient and sum add the contributions
-! to the appropriate components of the Cartesian gradient.
-              call sc_grad_scale(1.0d0-sss)
-            endif
-          enddo      ! j
+      dscj_inv=vbld_inv(j+nres)
+chi1=chi(itypi,itypj)
+chi2=chi(itypj,itypi)
+chi12=chi1*chi2
+chip1=chip(itypi)
+      alf1=alp(itypi)
+      alf2=alp(itypj)
+      alf12=0.5D0*(alf1+alf2)
+        xj=c(1,nres+j)-xi
+        yj=c(2,nres+j)-yi
+        zj=c(3,nres+j)-zi
+            call to_box(xj,yj,zj)
+            call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+            aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            xj=boxshift(xj-xi,boxxsize)
+            yj=boxshift(yj-yi,boxysize)
+            zj=boxshift(zj-zi,boxzsize)
+        dxj=dc_norm(1,nres+j)
+        dyj=dc_norm(2,nres+j)
+        dzj=dc_norm(3,nres+j)
+        rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+        rij=dsqrt(rrij)
+      sss=sscale(1.0d0/(rij*sigmaii(itypi,itypj)))
+
+        if (sss.lt.1.0d0) then
+
+        ! Calculate the angle-dependent terms of energy & contributions to derivatives.
+        call sc_angular
+        ! Calculate whole angle-dependent part of epsilon and contributions
+        ! to its derivatives
+        fac=(rrij*sigsq)**expon2
+        e1=fac*fac*aa_aq(itypi,itypj)
+        e2=fac*bb_aq(itypi,itypj)
+      evdwij=eps1*eps2rt*eps3rt*(e1+e2)
+        eps2der=evdwij*eps3rt
+        eps3der=evdwij*eps2rt
+        evdwij=evdwij*eps2rt*eps3rt
+      evdw=evdw+evdwij*(1.0d0-sss)
+        if (lprn) then
+        sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0)
+      epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj)
+        !d              write (iout,'(2(a3,i3,2x),15(0pf7.3))')
+        !d     &          restyp(itypi,1),i,restyp(itypj,1),j,
+        !d     &          epsi,sigm,chi1,chi2,chip1,chip2,
+        !d     &          eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq),
+        !d     &          om1,om2,om12,1.0D0/dsqrt(rrij),
+        !d     &          evdwij
+        endif
+        ! Calculate gradient components.
+        e1=e1*eps1*eps2rt**2*eps3rt**2
+      fac=-expon*(e1+evdwij)
+        sigder=fac/sigsq
+        fac=rrij*fac
+        ! Calculate radial part of the gradient
+        gg(1)=xj*fac
+        gg(2)=yj*fac
+        gg(3)=zj*fac
+        ! Calculate the angular part of the gradient and sum add the contributions
+        ! to the appropriate components of the Cartesian gradient.
+      call sc_grad_scale(1.0d0-sss)
+        endif
+        enddo      ! j
         enddo        ! iint
         enddo        ! iint
-      enddo          ! i
-!     stop
-      return
-      end subroutine ebp_long
-!-----------------------------------------------------------------------------
+        enddo          ! i
+        !     stop
+        return
+        end subroutine ebp_long
+        !-----------------------------------------------------------------------------
       subroutine ebp_short(evdw)
       subroutine ebp_short(evdw)
-!
-! This subroutine calculates the interaction energy of nonbonded side chains
-! assuming the Berne-Pechukas potential of interaction.
-!
-      use calc_data
+        !
+        ! This subroutine calculates the interaction energy of nonbonded side chains
+        ! assuming the Berne-Pechukas potential of interaction.
+        !
+        use calc_data
 !      implicit real*8 (a-h,o-z)
 !      implicit real*8 (a-h,o-z)
-!      include 'DIMENSIONS'
-!      include 'COMMON.GEO'
-!      include 'COMMON.VAR'
-!      include 'COMMON.LOCAL'
-!      include 'COMMON.CHAIN'
-!      include 'COMMON.DERIV'
-!      include 'COMMON.NAMES'
-!      include 'COMMON.INTERACT'
-!      include 'COMMON.IOUNITS'
-!      include 'COMMON.CALC'
-      use comm_srutu
-!el      integer :: icall
-!el      common /srutu/ icall
+        !      include 'DIMENSIONS'
+        !      include 'COMMON.GEO'
+        !      include 'COMMON.VAR'
+        !      include 'COMMON.LOCAL'
+        !      include 'COMMON.CHAIN'
+        !      include 'COMMON.DERIV'
+        !      include 'COMMON.NAMES'
+        !      include 'COMMON.INTERACT'
+        !      include 'COMMON.IOUNITS'
+        !      include 'COMMON.CALC'
+        use comm_srutu
+        !el      integer :: icall
+        !el      common /srutu/ icall
 !     double precision rrsave(maxdim)
 !     double precision rrsave(maxdim)
-      logical :: lprn
-!el local variables
-      integer :: iint,itypi,itypi1,itypj
-      real(kind=8) :: rrij,xi,yi,zi,fac,sigm,epsi
-      real(kind=8) :: sss,e1,e2,evdw
-      evdw=0.0D0
-!     print *,'Entering EBP nnt=',nnt,' nct=',nct,' expon=',expon
-      evdw=0.0D0
-!     if (icall.eq.0) then
-!       lprn=.true.
-!     else
+        logical :: lprn
+        !el local variables
+        integer :: iint,itypi,itypi1,itypj
+        real(kind=8) :: rrij,xi,yi,zi,fac,sigm,epsi
+        real(kind=8) :: sss,e1,e2,evdw,aa,bb, &
+        sslipi,ssgradlipi,sslipj,ssgradlipj
+        evdw=0.0D0
+        !     print *,'Entering EBP nnt=',nnt,' nct=',nct,' expon=',expon
+        evdw=0.0D0
+        !     if (icall.eq.0) then
+        !       lprn=.true.
+        !     else
         lprn=.false.
         lprn=.false.
-!     endif
-!el      ind=0
-      do i=iatsc_s,iatsc_e
-        itypi=itype(i,1)
+        !     endif
+        !el      ind=0
+        do i=iatsc_s,iatsc_e
+      itypi=itype(i,1)
         if (itypi.eq.ntyp1) cycle
         itypi1=itype(i+1,1)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         if (itypi.eq.ntyp1) cycle
         itypi1=itype(i+1,1)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
+        call to_box(xi,yi,zi)
+      call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
-!        dsci_inv=dsc_inv(itypi)
-        dsci_inv=vbld_inv(i+nres)
-!
-! Calculate SC interaction energy.
-!
+        !        dsci_inv=dsc_inv(itypi)
+      dsci_inv=vbld_inv(i+nres)
+        !
+        ! Calculate SC interaction energy.
+        !
         do iint=1,nint_gr(i)
         do iint=1,nint_gr(i)
-          do j=istart(i,iint),iend(i,iint)
-!el            ind=ind+1
-            itypj=itype(j,1)
-            if (itypj.eq.ntyp1) cycle
-!            dscj_inv=dsc_inv(itypj)
-            dscj_inv=vbld_inv(j+nres)
-            chi1=chi(itypi,itypj)
-            chi2=chi(itypj,itypi)
-            chi12=chi1*chi2
-            chip1=chip(itypi)
-            chip2=chip(itypj)
-            chip12=chip1*chip2
-            alf1=alp(itypi)
-            alf2=alp(itypj)
-            alf12=0.5D0*(alf1+alf2)
-            xj=c(1,nres+j)-xi
-            yj=c(2,nres+j)-yi
-            zj=c(3,nres+j)-zi
+      do j=istart(i,iint),iend(i,iint)
+        !el            ind=ind+1
+      itypj=itype(j,1)
+        if (itypj.eq.ntyp1) cycle
+        !            dscj_inv=dsc_inv(itypj)
+        dscj_inv=vbld_inv(j+nres)
+        chi1=chi(itypi,itypj)
+      chi2=chi(itypj,itypi)
+        chi12=chi1*chi2
+        chip1=chip(itypi)
+      chip2=chip(itypj)
+        chip12=chip1*chip2
+        alf1=alp(itypi)
+        alf2=alp(itypj)
+      alf12=0.5D0*(alf1+alf2)
+        xj=c(1,nres+j)-xi
+        yj=c(2,nres+j)-yi
+        zj=c(3,nres+j)-zi
+        call to_box(xj,yj,zj)
+      call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+        aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+        +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+        bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            xj=boxshift(xj-xi,boxxsize)
+            yj=boxshift(yj-yi,boxysize)
+            zj=boxshift(zj-zi,boxzsize)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
@@ -13932,35 +13887,8 @@
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
-          xi=mod(xi,boxxsize)
-          if (xi.lt.0) xi=xi+boxxsize
-          yi=mod(yi,boxysize)
-          if (yi.lt.0) yi=yi+boxysize
-          zi=mod(zi,boxzsize)
-          if (zi.lt.0) zi=zi+boxzsize
-       if ((zi.gt.bordlipbot)    &
-        .and.(zi.lt.bordliptop)) then
-!C the energy transfer exist
-        if (zi.lt.buflipbot) then
-!C what fraction I am in
-         fracinbuf=1.0d0-    &
-             ((zi-bordlipbot)/lipbufthick)
-!C lipbufthick is thickenes of lipid buffore
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
-        elseif (zi.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
-        else
-         sslipi=1.0d0
-         ssgradlipi=0.0
-        endif
-       else
-         sslipi=0.0d0
-         ssgradlipi=0.0
-       endif
-
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
@@ -14025,71 +13953,15 @@
             yj=c(2,nres+j)
             zj=c(3,nres+j)
 ! Searching for nearest neighbour
             yj=c(2,nres+j)
             zj=c(3,nres+j)
 ! Searching for nearest neighbour
-          xj=mod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=mod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=mod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-       if ((zj.gt.bordlipbot)   &
-      .and.(zj.lt.bordliptop)) then
-!C the energy transfer exist
-        if (zj.lt.buflipbot) then
-!C what fraction I am in
-         fracinbuf=1.0d0-  &
-             ((zj-bordlipbot)/lipbufthick)
-!C lipbufthick is thickenes of lipid buffore
-         sslipj=sscalelip(fracinbuf)
-         ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
-        elseif (zj.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
-         sslipj=sscalelip(fracinbuf)
-         ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
-        else
-         sslipj=1.0d0
-         ssgradlipj=0.0
-        endif
-       else
-         sslipj=0.0d0
-         ssgradlipj=0.0
-       endif
-      aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
-       +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
-      bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
-       +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
-
-          dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          xj_safe=xj
-          yj_safe=yj
-          zj_safe=zj
-          subchap=0
-          do xshift=-1,1
-          do yshift=-1,1
-          do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-          enddo
-          enddo
-          enddo
-          if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-          else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-          endif
-
+            call to_box(xj,yj,zj)
+            call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+            aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            xj=boxshift(xj-xi,boxxsize)
+            yj=boxshift(yj-yi,boxysize)
+            zj=boxshift(zj-zi,boxzsize)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
@@ -14212,34 +14084,8 @@
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
-          xi=mod(xi,boxxsize)
-          if (xi.lt.0) xi=xi+boxxsize
-          yi=mod(yi,boxysize)
-          if (yi.lt.0) yi=yi+boxysize
-          zi=mod(zi,boxzsize)
-          if (zi.lt.0) zi=zi+boxzsize
-       if ((zi.gt.bordlipbot)    &
-        .and.(zi.lt.bordliptop)) then
-!C the energy transfer exist
-        if (zi.lt.buflipbot) then
-!C what fraction I am in
-         fracinbuf=1.0d0-    &
-             ((zi-bordlipbot)/lipbufthick)
-!C lipbufthick is thickenes of lipid buffore
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
-        elseif (zi.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
-        else
-         sslipi=1.0d0
-         ssgradlipi=0.0
-        endif
-       else
-         sslipi=0.0d0
-         ssgradlipi=0.0
-       endif
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
 
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
 
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
@@ -14252,11 +14098,6 @@
         dzi=dc_norm(3,nres+i)
 !        dsci_inv=dsc_inv(itypi)
         dsci_inv=vbld_inv(i+nres)
         dzi=dc_norm(3,nres+i)
 !        dsci_inv=dsc_inv(itypi)
         dsci_inv=vbld_inv(i+nres)
-!        write (iout,*) "i",i,dsc_inv(itypi),dsci_inv,1.0d0/vbld(i+nres)
-!        write (iout,*) "dcnori",dxi*dxi+dyi*dyi+dzi*dzi
-!
-! Calculate SC interaction energy.
-!
         do iint=1,nint_gr(i)
           do j=istart(i,iint),iend(i,iint)
             IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
         do iint=1,nint_gr(i)
           do j=istart(i,iint),iend(i,iint)
             IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
@@ -14285,15 +14126,13 @@
                             'evdw',i,j,evdwij,'tss'
               endif!dyn_ss_mask(k)
              enddo! k
                             'evdw',i,j,evdwij,'tss'
               endif!dyn_ss_mask(k)
              enddo! k
-
-!              if (energy_dec) write (iout,*) &
-!                              'evdw',i,j,evdwij,' ss'
             ELSE
             ELSE
-!el            ind=ind+1
-            itypj=itype(j,1)
+
+!          typj=itype(j,1)
             if (itypj.eq.ntyp1) cycle
 !            dscj_inv=dsc_inv(itypj)
             dscj_inv=vbld_inv(j+nres)
             if (itypj.eq.ntyp1) cycle
 !            dscj_inv=dsc_inv(itypj)
             dscj_inv=vbld_inv(j+nres)
+            dscj_inv=dsc_inv(itypj)
 !            write (iout,*) "j",j,dsc_inv(itypj),dscj_inv,
 !     &       1.0d0/vbld(j+nres)
 !            write (iout,*) "i",i," j", j," itype",itype(i,1),itype(j,1)
 !            write (iout,*) "j",j,dsc_inv(itypj),dscj_inv,
 !     &       1.0d0/vbld(j+nres)
 !            write (iout,*) "i",i," j", j," itype",itype(i,1),itype(j,1)
@@ -14314,72 +14153,15 @@
             yj=c(2,nres+j)
             zj=c(3,nres+j)
 ! Searching for nearest neighbour
             yj=c(2,nres+j)
             zj=c(3,nres+j)
 ! Searching for nearest neighbour
-          xj=mod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=mod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=mod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-       if ((zj.gt.bordlipbot)   &
-      .and.(zj.lt.bordliptop)) then
-!C the energy transfer exist
-        if (zj.lt.buflipbot) then
-!C what fraction I am in
-         fracinbuf=1.0d0-  &
-             ((zj-bordlipbot)/lipbufthick)
-!C lipbufthick is thickenes of lipid buffore
-         sslipj=sscalelip(fracinbuf)
-         ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
-        elseif (zj.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
-         sslipj=sscalelip(fracinbuf)
-         ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
-        else
-         sslipj=1.0d0
-         ssgradlipj=0.0
-        endif
-       else
-         sslipj=0.0d0
-         ssgradlipj=0.0
-       endif
-      aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
-       +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
-      bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
-       +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
-
-          dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          xj_safe=xj
-          yj_safe=yj
-          zj_safe=zj
-          subchap=0
-
-          do xshift=-1,1
-          do yshift=-1,1
-          do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-          enddo
-          enddo
-          enddo
-          if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-          else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-          endif
-
+            call to_box(xj,yj,zj)
+            call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+            aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+             +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            xj=boxshift(xj-xi,boxxsize)
+            yj=boxshift(yj-yi,boxysize)
+            zj=boxshift(zj-zi,boxzsize)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
@@ -14487,7 +14269,8 @@
       logical :: lprn
 !el local variables
       integer :: iint,itypi,itypi1,itypj
       logical :: lprn
 !el local variables
       integer :: iint,itypi,itypi1,itypj
-      real(kind=8) :: rrij,xi,yi,zi,fac,sigm,epsi,r0ij,sig,sig0ij
+      real(kind=8) :: rrij,xi,yi,zi,fac,sigm,epsi,r0ij,sig,sig0ij,&
+                      sslipi,ssgradlipi,sslipj,ssgradlipj,aa,bb
       real(kind=8) :: sss,e1,e2,evdw,fac_augm,e_augm,rij_shift
       evdw=0.0D0
 !     print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
       real(kind=8) :: sss,e1,e2,evdw,fac_augm,e_augm,rij_shift
       evdw=0.0D0
 !     print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
@@ -14502,9 +14285,12 @@
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
+
 !        dsci_inv=dsc_inv(itypi)
         dsci_inv=vbld_inv(i+nres)
 !
 !        dsci_inv=dsc_inv(itypi)
         dsci_inv=vbld_inv(i+nres)
 !
@@ -14531,6 +14317,15 @@
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
+            call to_box(xj,yj,zj)
+            call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+            aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+            +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+            +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            xj=boxshift(xj-xi,boxxsize)
+            yj=boxshift(yj-yi,boxysize)
+            zj=boxshift(zj-zi,boxzsize)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
@@ -14616,7 +14411,8 @@
       logical :: lprn
 !el local variables
       integer :: iint,itypi,itypi1,itypj
       logical :: lprn
 !el local variables
       integer :: iint,itypi,itypi1,itypj
-      real(kind=8) :: rrij,xi,yi,zi,fac,sigm,epsi,rij_shift
+      real(kind=8) :: rrij,xi,yi,zi,fac,sigm,epsi,rij_shift,&
+                      sslipi,ssgradlipi, sslipj,ssgradlipj,aa,bb
       real(kind=8) :: sss,e1,e2,evdw,r0ij,sig,sig0ij,fac_augm,e_augm
       evdw=0.0D0
 !     print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
       real(kind=8) :: sss,e1,e2,evdw,r0ij,sig,sig0ij,fac_augm,e_augm
       evdw=0.0D0
 !     print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
@@ -14634,6 +14430,8 @@
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
 !        dsci_inv=dsc_inv(itypi)
         dsci_inv=vbld_inv(i+nres)
 !
 !        dsci_inv=dsc_inv(itypi)
         dsci_inv=vbld_inv(i+nres)
 !
@@ -14660,6 +14458,15 @@
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
+            call to_box(xj,yj,zj)
+            call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+            aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+            +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+            +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+            xj=boxshift(xj-xi,boxxsize)
+            yj=boxshift(yj-yi,boxysize)
+            zj=boxshift(zj-zi,boxzsize)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
             dxj=dc_norm(1,nres+j)
             dyj=dc_norm(2,nres+j)
             dzj=dc_norm(3,nres+j)
@@ -14860,12 +14667,8 @@
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
-          xmedi=dmod(xmedi,boxxsize)
-          if (xmedi.lt.0) xmedi=xmedi+boxxsize
-          ymedi=dmod(ymedi,boxysize)
-          if (ymedi.lt.0) ymedi=ymedi+boxysize
-          zmedi=dmod(zmedi,boxzsize)
-          if (zmedi.lt.0) zmedi=zmedi+boxzsize
+        call to_box(xmedi,ymedi,zmedi)
+        call lipid_layer(xmedi,ymedi,zmedi,sslipi,ssgradlipi)
         num_conti=0
         call eelecij_scale(i,i+2,ees,evdw1,eel_loc)
         if (wturn3.gt.0.0d0) call eturn3(i,eello_turn3)
         num_conti=0
         call eelecij_scale(i,i+2,ees,evdw1,eel_loc)
         if (wturn3.gt.0.0d0) call eturn3(i,eello_turn3)
@@ -14884,12 +14687,10 @@
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
-          xmedi=dmod(xmedi,boxxsize)
-          if (xmedi.lt.0) xmedi=xmedi+boxxsize
-          ymedi=dmod(ymedi,boxysize)
-          if (ymedi.lt.0) ymedi=ymedi+boxysize
-          zmedi=dmod(zmedi,boxzsize)
-          if (zmedi.lt.0) zmedi=zmedi+boxzsize
+
+        call to_box(xmedi,ymedi,zmedi)
+        call lipid_layer(xmedi,ymedi,zmedi,sslipi,ssgradlipi)
+
         num_conti=num_cont_hb(i)
         call eelecij_scale(i,i+3,ees,evdw1,eel_loc)
         if (wturn4.gt.0.0d0 .and. itype(i+2,1).ne.ntyp1) &
         num_conti=num_cont_hb(i)
         call eelecij_scale(i,i+3,ees,evdw1,eel_loc)
         if (wturn4.gt.0.0d0 .and. itype(i+2,1).ne.ntyp1) &
@@ -14910,12 +14711,8 @@
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
-          xmedi=dmod(xmedi,boxxsize)
-          if (xmedi.lt.0) xmedi=xmedi+boxxsize
-          ymedi=dmod(ymedi,boxysize)
-          if (ymedi.lt.0) ymedi=ymedi+boxysize
-          zmedi=dmod(zmedi,boxzsize)
-          if (zmedi.lt.0) zmedi=zmedi+boxzsize
+        call to_box(xmedi,ymedi,zmedi)
+        call lipid_layer(xmedi,ymedi,zmedi,sslipi,ssgradlipi)
 !        write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
         num_conti=num_cont_hb(i)
         do j=ielstart(i),ielend(i)
 !        write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
         num_conti=num_cont_hb(i)
         do j=ielstart(i),ielend(i)
@@ -14994,7 +14791,7 @@
                   ury,urz,vry,vrz,a22der,a23der,a32der,a33der,cosa4,&
                   wij,cosbg1,cosbg2,ees0pij,ees0mij,fac3p,ecosa1,ecosb1,&
                   ecosg1,ecosa2,ecosb2,ecosg2,ecosap,ecosbp,ecosgp,&
                   ury,urz,vry,vrz,a22der,a23der,a32der,a33der,cosa4,&
                   wij,cosbg1,cosbg2,ees0pij,ees0mij,fac3p,ecosa1,ecosb1,&
                   ecosg1,ecosa2,ecosb2,ecosg2,ecosap,ecosbp,ecosgp,&
-                  ecosam,ecosbm,ecosgm,ghalf,time00
+                  ecosam,ecosbm,ecosgm,ghalf,time00,faclipij,faclipij2
 !      integer :: maxconts
 !      maxconts = nres/4
 !      allocate(gacontp_hb1(3,maxconts,nres)) !(3,maxconts,maxres)  ! (maxconts=maxres/4)
 !      integer :: maxconts
 !      maxconts = nres/4
 !      allocate(gacontp_hb1(3,maxconts,nres)) !(3,maxconts,maxres)  ! (maxconts=maxres/4)
@@ -15038,45 +14835,13 @@
           xj=c(1,j)+0.5D0*dxj
           yj=c(2,j)+0.5D0*dyj
           zj=c(3,j)+0.5D0*dzj
           xj=c(1,j)+0.5D0*dxj
           yj=c(2,j)+0.5D0*dyj
           zj=c(3,j)+0.5D0*dzj
-          xj=mod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=mod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=mod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-      isubchap=0
-      dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
-      xj_safe=xj
-      yj_safe=yj
-      zj_safe=zj
-      do xshift=-1,1
-      do yshift=-1,1
-      do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            isubchap=1
-          endif
-       enddo
-       enddo
-       enddo
-       if (isubchap.eq.1) then
-!C          print *,i,j
-          xj=xj_temp-xmedi
-          yj=yj_temp-ymedi
-          zj=zj_temp-zmedi
-       else
-          xj=xj_safe-xmedi
-          yj=yj_safe-ymedi
-          zj=zj_safe-zmedi
-       endif
-
+          call to_box(xj,yj,zj)
+          call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+          faclipij=(sslipi+sslipj)/2.0d0*lipscale+1.0d0
+          faclipij2=(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0
+          xj=boxshift(xj-xmedi,boxxsize)
+          yj=boxshift(yj-ymedi,boxysize)
+          zj=boxshift(zj-zmedi,boxzsize)
           rij=xj*xj+yj*yj+zj*zj
           rrmij=1.0D0/rij
           rij=dsqrt(rij)
           rij=xj*xj+yj*yj+zj*zj
           rrmij=1.0D0/rij
           rij=dsqrt(rij)
@@ -15771,7 +15536,8 @@
                  dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,&
                  dx_normj,dy_normj,dz_normj,rmij,ev1,ev2,evdwij,facvdw
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
                  dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,&
                  dx_normj,dy_normj,dz_normj,rmij,ev1,ev2,evdwij,facvdw
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
-                    dist_temp, dist_init,sss_grad
+                    dist_temp, dist_init,sss_grad,sslipi,ssgradlipi,&
+                   sslipj,ssgradlipj,faclipij2
       integer xshift,yshift,zshift
 
 
       integer xshift,yshift,zshift
 
 
@@ -15790,12 +15556,8 @@
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
-          xmedi=dmod(xmedi,boxxsize)
-          if (xmedi.lt.0) xmedi=xmedi+boxxsize
-          ymedi=dmod(ymedi,boxysize)
-          if (ymedi.lt.0) ymedi=ymedi+boxysize
-          zmedi=dmod(zmedi,boxzsize)
-          if (zmedi.lt.0) zmedi=zmedi+boxzsize
+        call to_box(xmedi,ymedi,zmedi)
+        call lipid_layer(xmedi,ymedi,zmedi,sslipi,ssgradlipi)
         num_conti=0
 !        write (iout,*) 'i',i,' ielstart',ielstart_vdw(i),
 !     &   ' ielend',ielend_vdw(i)
         num_conti=0
 !        write (iout,*) 'i',i,' ielstart',ielstart_vdw(i),
 !     &   ' ielend',ielend_vdw(i)
@@ -15820,45 +15582,12 @@
           xj=c(1,j)+0.5D0*dxj
           yj=c(2,j)+0.5D0*dyj
           zj=c(3,j)+0.5D0*dzj
           xj=c(1,j)+0.5D0*dxj
           yj=c(2,j)+0.5D0*dyj
           zj=c(3,j)+0.5D0*dzj
-          xj=mod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=mod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=mod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-      isubchap=0
-      dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
-      xj_safe=xj
-      yj_safe=yj
-      zj_safe=zj
-      do xshift=-1,1
-      do yshift=-1,1
-      do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            isubchap=1
-          endif
-       enddo
-       enddo
-       enddo
-       if (isubchap.eq.1) then
-!C          print *,i,j
-          xj=xj_temp-xmedi
-          yj=yj_temp-ymedi
-          zj=zj_temp-zmedi
-       else
-          xj=xj_safe-xmedi
-          yj=yj_safe-ymedi
-          zj=zj_safe-zmedi
-       endif
-
+          call to_box(xj,yj,zj)
+          call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+          faclipij2=(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0
+          xj=boxshift(xj-xmedi,boxxsize)
+          yj=boxshift(yj-ymedi,boxysize)
+          zj=boxshift(zj-zmedi,boxzsize)
           rij=xj*xj+yj*yj+zj*zj
           rrmij=1.0D0/rij
           rij=dsqrt(rij)
           rij=xj*xj+yj*yj+zj*zj
           rrmij=1.0D0/rij
           rij=dsqrt(rij)
@@ -15939,13 +15668,7 @@
         xi=0.5D0*(c(1,i)+c(1,i+1))
         yi=0.5D0*(c(2,i)+c(2,i+1))
         zi=0.5D0*(c(3,i)+c(3,i+1))
         xi=0.5D0*(c(1,i)+c(1,i+1))
         yi=0.5D0*(c(2,i)+c(2,i+1))
         zi=0.5D0*(c(3,i)+c(3,i+1))
-          xi=mod(xi,boxxsize)
-          if (xi.lt.0) xi=xi+boxxsize
-          yi=mod(yi,boxysize)
-          if (yi.lt.0) yi=yi+boxysize
-          zi=mod(zi,boxzsize)
-          if (zi.lt.0) zi=zi+boxzsize
-
+        call to_box(xi,yi,zi)
         do iint=1,nscp_gr(i)
 
         do j=iscpstart(i,iint),iscpend(i,iint)
         do iint=1,nscp_gr(i)
 
         do j=iscpstart(i,iint),iscpend(i,iint)
@@ -15959,43 +15682,10 @@
           xj=c(1,j)
           yj=c(2,j)
           zj=c(3,j)
           xj=c(1,j)
           yj=c(2,j)
           zj=c(3,j)
-          xj=mod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=mod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=mod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-      dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-      xj_safe=xj
-      yj_safe=yj
-      zj_safe=zj
-      subchap=0
-      do xshift=-1,1
-      do yshift=-1,1
-      do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-       enddo
-       enddo
-       enddo
-       if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-       else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-       endif
+          call to_box(xj,yj,zj)
+          xj=boxshift(xj-xi,boxxsize)
+          yj=boxshift(yj-yi,boxysize)
+          zj=boxshift(zj-zi,boxzsize)
           rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
 
           rij=dsqrt(1.0d0/rrij)
           rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
 
           rij=dsqrt(1.0d0/rrij)
@@ -16098,12 +15788,8 @@
         xi=0.5D0*(c(1,i)+c(1,i+1))
         yi=0.5D0*(c(2,i)+c(2,i+1))
         zi=0.5D0*(c(3,i)+c(3,i+1))
         xi=0.5D0*(c(1,i)+c(1,i+1))
         yi=0.5D0*(c(2,i)+c(2,i+1))
         zi=0.5D0*(c(3,i)+c(3,i+1))
-          xi=mod(xi,boxxsize)
-          if (xi.lt.0) xi=xi+boxxsize
-          yi=mod(yi,boxysize)
-          if (yi.lt.0) yi=yi+boxysize
-          zi=mod(zi,boxzsize)
-          if (zi.lt.0) zi=zi+boxzsize
+        call to_box(xi,yi,zi) 
+        if (zi.lt.0) zi=zi+boxzsize
 
         do iint=1,nscp_gr(i)
 
 
         do iint=1,nscp_gr(i)
 
@@ -16121,44 +15807,10 @@
           xj=c(1,j)
           yj=c(2,j)
           zj=c(3,j)
           xj=c(1,j)
           yj=c(2,j)
           zj=c(3,j)
-          xj=mod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=mod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=mod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-      dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-      xj_safe=xj
-      yj_safe=yj
-      zj_safe=zj
-      subchap=0
-      do xshift=-1,1
-      do yshift=-1,1
-      do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-       enddo
-       enddo
-       enddo
-       if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-       else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-       endif
-
+          call to_box(xj,yj,zj)
+          xj=boxshift(xj-xi,boxxsize)
+          yj=boxshift(yj-yi,boxysize)
+          zj=boxshift(zj-zi,boxzsize)
           rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
           rij=dsqrt(1.0d0/rrij)
             sss_ele_cut=sscale_ele(rij)
           rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
           rij=dsqrt(1.0d0/rrij)
             sss_ele_cut=sscale_ele(rij)
@@ -16710,7 +16362,7 @@
 ! Calculate the short-range part of ESCp
 !
       if (ipot.lt.6) then
 ! Calculate the short-range part of ESCp
 !
       if (ipot.lt.6) then
-        call escp_short(evdw2,evdw2_14)
+       call escp_short(evdw2,evdw2_14)
       endif
 !
 ! Calculate the bond-stretching energy
       endif
 !
 ! Calculate the bond-stretching energy
@@ -16730,14 +16382,14 @@
 !
       if (wang.gt.0d0) then
        if (tor_mode.eq.0) then
 !
       if (wang.gt.0d0) then
        if (tor_mode.eq.0) then
-         call ebend(ebe)
+           call ebend(ebe)
        else
 !C ebend kcc is Kubo cumulant clustered rigorous attemp to derive the
 !C energy function
        else
 !C ebend kcc is Kubo cumulant clustered rigorous attemp to derive the
 !C energy function
-         call ebend_kcc(ebe)
+        call ebend_kcc(ebe)
        endif
       else
        endif
       else
-        ebe=0.0d0
+          ebe=0.0d0
       endif
       ethetacnstr=0.0d0
       if (with_theta_constr) call etheta_constr(ethetacnstr)
       endif
       ethetacnstr=0.0d0
       if (with_theta_constr) call etheta_constr(ethetacnstr)
@@ -16764,13 +16416,13 @@
       if (wtor.gt.0.0d0) then
          if (tor_mode.eq.0) then
            call etor(etors)
       if (wtor.gt.0.0d0) then
          if (tor_mode.eq.0) then
            call etor(etors)
-         else
+          else
 !C etor kcc is Kubo cumulant clustered rigorous attemp to derive the
 !C energy function
 !C etor kcc is Kubo cumulant clustered rigorous attemp to derive the
 !C energy function
-           call etor_kcc(etors)
+        call etor_kcc(etors)
          endif
       else
          endif
       else
-        etors=0.0d0
+           etors=0.0d0
       endif
       edihcnstr=0.0d0
       if (ndih_constr.gt.0) call etor_constr(edihcnstr)
       endif
       edihcnstr=0.0d0
       if (ndih_constr.gt.0) call etor_constr(edihcnstr)
@@ -16787,15 +16439,15 @@
 ! 21/5/07 Calculate local sicdechain correlation energy
 !
       if (wsccor.gt.0.0d0) then
 ! 21/5/07 Calculate local sicdechain correlation energy
 !
       if (wsccor.gt.0.0d0) then
-        call eback_sc_corr(esccor)
+       call eback_sc_corr(esccor)
       else
       else
-        esccor=0.0d0
+       esccor=0.0d0
       endif
 !
 ! Put energy components into an array
 !
       do i=1,n_ene
       endif
 !
 ! Put energy components into an array
 !
       do i=1,n_ene
-        energia(i)=0.0d0
+       energia(i)=0.0d0
       enddo
       energia(1)=evdw
 #ifdef SCP14
       enddo
       energia(1)=evdw
 #ifdef SCP14
@@ -16835,9 +16487,9 @@
       if (y.lt.ymin) then
         gnmr1=(ymin-y)**wykl/wykl
       else if (y.gt.ymax) then
       if (y.lt.ymin) then
         gnmr1=(ymin-y)**wykl/wykl
       else if (y.gt.ymax) then
-        gnmr1=(y-ymax)**wykl/wykl
+       gnmr1=(y-ymax)**wykl/wykl
       else
       else
-        gnmr1=0.0d0
+       gnmr1=0.0d0
       endif
       return
       end function gnmr1
       endif
       return
       end function gnmr1
@@ -16847,11 +16499,11 @@
       real(kind=8) :: y,ymin,ymax
       real(kind=8) :: wykl=4.0d0
       if (y.lt.ymin) then
       real(kind=8) :: y,ymin,ymax
       real(kind=8) :: wykl=4.0d0
       if (y.lt.ymin) then
-        gnmr1prim=-(ymin-y)**(wykl-1)
+       gnmr1prim=-(ymin-y)**(wykl-1)
       else if (y.gt.ymax) then
       else if (y.gt.ymax) then
-        gnmr1prim=(y-ymax)**(wykl-1)
+       gnmr1prim=(y-ymax)**(wykl-1)
       else
       else
-        gnmr1prim=0.0d0
+       gnmr1prim=0.0d0
       endif
       return
       end function gnmr1prim
       endif
       return
       end function gnmr1prim
@@ -16862,7 +16514,7 @@
       if (y.lt.ymin) then
         rlornmr1=(ymin-y)**wykl/((ymin-y)**wykl+sigma**wykl)
       else if (y.gt.ymax) then
       if (y.lt.ymin) then
         rlornmr1=(ymin-y)**wykl/((ymin-y)**wykl+sigma**wykl)
       else if (y.gt.ymax) then
-        rlornmr1=(y-ymax)**wykl/((y-ymax)**wykl+sigma**wykl)
+       rlornmr1=(y-ymax)**wykl/((y-ymax)**wykl+sigma**wykl)
       else
         rlornmr1=0.0d0
       endif
       else
         rlornmr1=0.0d0
       endif
@@ -16876,10 +16528,10 @@
         rlornmr1prim=-(ymin-y)**(wykl-1)*sigma**wykl*wykl/ &
         ((ymin-y)**wykl+sigma**wykl)**2
       else if (y.gt.ymax) then
         rlornmr1prim=-(ymin-y)**(wykl-1)*sigma**wykl*wykl/ &
         ((ymin-y)**wykl+sigma**wykl)**2
       else if (y.gt.ymax) then
-        rlornmr1prim=(y-ymax)**(wykl-1)*sigma**wykl*wykl/ &
+         rlornmr1prim=(y-ymax)**(wykl-1)*sigma**wykl*wykl/ &
         ((y-ymax)**wykl+sigma**wykl)**2
       else
         ((y-ymax)**wykl+sigma**wykl)**2
       else
-        rlornmr1prim=0.0d0
+       rlornmr1prim=0.0d0
       endif
       return
       end function rlornmr1prim
       endif
       return
       end function rlornmr1prim
@@ -16954,18 +16606,18 @@
       gthetai=0.0D0
       gphii=0.0D0
       do j=i+1,nres-1
       gthetai=0.0D0
       gphii=0.0D0
       do j=i+1,nres-1
-          ind=ind+1
+        ind=ind+1
 !         ind=indmat(i,j)
 !         print *,'GRAD: i=',i,' jc=',j,' ind=',ind
 !         ind=indmat(i,j)
 !         print *,'GRAD: i=',i,' jc=',j,' ind=',ind
-        do k=1,3
-            gthetai=gthetai+dcdv(k,ind)*gradc(k,j,icg)
-          enddo
-        do k=1,3
-          gphii=gphii+dcdv(k+3,ind)*gradc(k,j,icg)
-          enddo
+       do k=1,3
+       gthetai=gthetai+dcdv(k,ind)*gradc(k,j,icg)
         enddo
         enddo
+        do k=1,3
+        gphii=gphii+dcdv(k+3,ind)*gradc(k,j,icg)
+         enddo
+       enddo
       do j=i+1,nres-1
       do j=i+1,nres-1
-          ind1=ind1+1
+        ind1=ind1+1
 !         ind1=indmat(i,j)
 !         print *,'GRAD: i=',i,' jx=',j,' ind1=',ind1
         do k=1,3
 !         ind1=indmat(i,j)
 !         print *,'GRAD: i=',i,' jx=',j,' ind1=',ind1
         do k=1,3
@@ -17063,12 +16715,13 @@
 !      include 'COMMON.TIME1'
 !
       integer :: i,j
 !      include 'COMMON.TIME1'
 !
       integer :: i,j
+      real(kind=8) :: time00,time01
 
 ! This subrouting calculates total Cartesian coordinate gradient. 
 ! The subroutine chainbuild_cart and energy MUST be called beforehand.
 !
 !#define DEBUG
 
 ! This subrouting calculates total Cartesian coordinate gradient. 
 ! The subroutine chainbuild_cart and energy MUST be called beforehand.
 !
 !#define DEBUG
-#ifdef TIMING
+#ifdef TIMINGtime01
       time00=MPI_Wtime()
 #endif
       icg=1
       time00=MPI_Wtime()
 #endif
       icg=1
@@ -17078,7 +16731,7 @@
 !#define DEBUG
 !el      write (iout,*) "After sum_gradient"
 #ifdef DEBUG
 !#define DEBUG
 !el      write (iout,*) "After sum_gradient"
 #ifdef DEBUG
-!el      write (iout,*) "After sum_gradient"
+      write (iout,*) "After sum_gradient"
       do i=1,nres-1
         write (iout,*) i," gradc  ",(gradc(j,i,icg),j=1,3)
         write (iout,*) i," gradx  ",(gradx(j,i,icg),j=1,3)
       do i=1,nres-1
         write (iout,*) i," gradc  ",(gradc(j,i,icg),j=1,3)
         write (iout,*) i," gradx  ",(gradx(j,i,icg),j=1,3)
@@ -17122,8 +16775,8 @@
 !          if (i.le.2) print *,"gcart_one",gcart(j,i),gradc(j,i,icg)
         enddo
 #ifdef DEBUG
 !          if (i.le.2) print *,"gcart_one",gcart(j,i),gradc(j,i,icg)
         enddo
 #ifdef DEBUG
-        write (iout,'(i5,2(3f10.5,5x),f10.5)') i,(gcart(j,i),j=1,3),&
-          (gxcart(j,i),j=1,3),gloc(i,icg)
+        write (iout,'(i5,2(3f10.5,5x),4f10.5)') i,(gcart(j,i),j=1,3),&
+          (gxcart(j,i),j=1,3),gloc(i,icg),(gloc_sc(j,i,icg),j=1,3)
 #endif
       enddo
 #ifdef TIMING
 #endif
       enddo
 #ifdef TIMING
@@ -17140,7 +16793,7 @@
             write (iout,*) "gcart and gxcart after int_to_cart"
             do i=0,nres-1
             write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3),&
             write (iout,*) "gcart and gxcart after int_to_cart"
             do i=0,nres-1
             write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3),&
-                (gxcart(j,i),j=1,3)
+            (gxcart(j,i),j=1,3)
             enddo
 #endif
 !#undef DEBUG
             enddo
 #endif
 !#undef DEBUG
@@ -17160,24 +16813,24 @@
             if (nnt.gt.1) then
               do j=1,3
       !            gcart_new(j,nnt)=gcart_new(j,nnt)+gcart_new(j,1)
             if (nnt.gt.1) then
               do j=1,3
       !            gcart_new(j,nnt)=gcart_new(j,nnt)+gcart_new(j,1)
-                gcart(j,nnt)=gcart(j,nnt)+gcart(j,1)
-              enddo
-            endif
-            if (nct.lt.nres) then
-              do j=1,3
+            gcart(j,nnt)=gcart(j,nnt)+gcart(j,1)
+            enddo
+          endif
+          if (nct.lt.nres) then
+            do j=1,3
       !            gcart_new(j,nct)=gcart_new(j,nct)+gcart_new(j,nres)
       !            gcart_new(j,nct)=gcart_new(j,nct)+gcart_new(j,nres)
-                gcart(j,nct)=gcart(j,nct)+gcart(j,nres)
-              enddo
-            endif
+            gcart(j,nct)=gcart(j,nct)+gcart(j,nres)
+            enddo
+          endif
 #endif
 #ifdef TIMING
 #endif
 #ifdef TIMING
-            time_cartgrad=time_cartgrad+MPI_Wtime()-time00
+          time_cartgrad=time_cartgrad+MPI_Wtime()-time00
 #endif
 !#undef DEBUG
 #endif
 !#undef DEBUG
-            return
-            end subroutine cartgrad
+          return
+          end subroutine cartgrad
       !-----------------------------------------------------------------------------
       !-----------------------------------------------------------------------------
-            subroutine zerograd
+          subroutine zerograd
       !      implicit real*8 (a-h,o-z)
       !      include 'DIMENSIONS'
       !      include 'COMMON.DERIV'
       !      implicit real*8 (a-h,o-z)
       !      include 'DIMENSIONS'
       !      include 'COMMON.DERIV'
@@ -17187,7 +16840,7 @@
       !      include 'COMMON.SCCOR'
       !
       !el local variables
       !      include 'COMMON.SCCOR'
       !
       !el local variables
-            integer :: i,j,intertyp,k
+          integer :: i,j,intertyp,k
       ! Initialize Cartesian-coordinate gradient
       !
       !      if (.not.allocated(gradx)) allocate(gradx(3,nres,2)) !(3,maxres,2)
       ! Initialize Cartesian-coordinate gradient
       !
       !      if (.not.allocated(gradx)) allocate(gradx(3,nres,2)) !(3,maxres,2)
@@ -17221,114 +16874,116 @@
       !      allocate(dXX_XYZtab(3,nres),dYY_XYZtab(3,nres),dZZ_XYZtab(3,nres))      !(3,maxres)
       !      common /mpgrad/
       !      allocate(jgrad_start(nres),jgrad_end(nres)) !(maxres)
       !      allocate(dXX_XYZtab(3,nres),dYY_XYZtab(3,nres),dZZ_XYZtab(3,nres))      !(3,maxres)
       !      common /mpgrad/
       !      allocate(jgrad_start(nres),jgrad_end(nres)) !(maxres)
-              
-              
+            
+            
 
       !          gradc(j,i,icg)=0.0d0
       !          gradx(j,i,icg)=0.0d0
 
       !      allocate(gloc_sc(3,nres,10)) !(3,0:maxres2,10)maxres2=2*maxres
       !elwrite(iout,*) "icg",icg
 
       !          gradc(j,i,icg)=0.0d0
       !          gradx(j,i,icg)=0.0d0
 
       !      allocate(gloc_sc(3,nres,10)) !(3,0:maxres2,10)maxres2=2*maxres
       !elwrite(iout,*) "icg",icg
-            do i=-1,nres
-            do j=1,3
-              gvdwx(j,i)=0.0D0
-              gradx_scp(j,i)=0.0D0
-              gvdwc(j,i)=0.0D0
-              gvdwc_scp(j,i)=0.0D0
-              gvdwc_scpp(j,i)=0.0d0
-              gelc(j,i)=0.0D0
-              gelc_long(j,i)=0.0D0
-              gradb(j,i)=0.0d0
-              gradbx(j,i)=0.0d0
-              gvdwpp(j,i)=0.0d0
-              gel_loc(j,i)=0.0d0
-              gel_loc_long(j,i)=0.0d0
-              ghpbc(j,i)=0.0D0
-              ghpbx(j,i)=0.0D0
-              gcorr3_turn(j,i)=0.0d0
-              gcorr4_turn(j,i)=0.0d0
-              gradcorr(j,i)=0.0d0
-              gradcorr_long(j,i)=0.0d0
-              gradcorr5_long(j,i)=0.0d0
-              gradcorr6_long(j,i)=0.0d0
-              gcorr6_turn_long(j,i)=0.0d0
-              gradcorr5(j,i)=0.0d0
-              gradcorr6(j,i)=0.0d0
-              gcorr6_turn(j,i)=0.0d0
-              gsccorc(j,i)=0.0d0
-              gsccorx(j,i)=0.0d0
-              gradc(j,i,icg)=0.0d0
-              gradx(j,i,icg)=0.0d0
-              gscloc(j,i)=0.0d0
-              gsclocx(j,i)=0.0d0
-              gliptran(j,i)=0.0d0
-              gliptranx(j,i)=0.0d0
-              gliptranc(j,i)=0.0d0
-              gshieldx(j,i)=0.0d0
-              gshieldc(j,i)=0.0d0
-              gshieldc_loc(j,i)=0.0d0
-              gshieldx_ec(j,i)=0.0d0
-              gshieldc_ec(j,i)=0.0d0
-              gshieldc_loc_ec(j,i)=0.0d0
-              gshieldx_t3(j,i)=0.0d0
-              gshieldc_t3(j,i)=0.0d0
-              gshieldc_loc_t3(j,i)=0.0d0
-              gshieldx_t4(j,i)=0.0d0
-              gshieldc_t4(j,i)=0.0d0
-              gshieldc_loc_t4(j,i)=0.0d0
-              gshieldx_ll(j,i)=0.0d0
-              gshieldc_ll(j,i)=0.0d0
-              gshieldc_loc_ll(j,i)=0.0d0
-              gg_tube(j,i)=0.0d0
-              gg_tube_sc(j,i)=0.0d0
-              gradafm(j,i)=0.0d0
-              gradb_nucl(j,i)=0.0d0
-              gradbx_nucl(j,i)=0.0d0
-              gvdwpp_nucl(j,i)=0.0d0
-              gvdwpp(j,i)=0.0d0
-              gelpp(j,i)=0.0d0
-              gvdwpsb(j,i)=0.0d0
-              gvdwpsb1(j,i)=0.0d0
-              gvdwsbc(j,i)=0.0d0
-              gvdwsbx(j,i)=0.0d0
-              gelsbc(j,i)=0.0d0
-              gradcorr_nucl(j,i)=0.0d0
-              gradcorr3_nucl(j,i)=0.0d0
-              gradxorr_nucl(j,i)=0.0d0
-              gradxorr3_nucl(j,i)=0.0d0
-              gelsbx(j,i)=0.0d0
-              gsbloc(j,i)=0.0d0
-              gsblocx(j,i)=0.0d0
-              gradpepcat(j,i)=0.0d0
-              gradpepcatx(j,i)=0.0d0
-              gradcatcat(j,i)=0.0d0
-              gvdwx_scbase(j,i)=0.0d0
-              gvdwc_scbase(j,i)=0.0d0
-              gvdwx_pepbase(j,i)=0.0d0
-              gvdwc_pepbase(j,i)=0.0d0
-              gvdwx_scpho(j,i)=0.0d0
-              gvdwc_scpho(j,i)=0.0d0
-              gvdwc_peppho(j,i)=0.0d0
-            enddo
-             enddo
-            do i=0,nres
-            do j=1,3
-              do intertyp=1,3
-               gloc_sc(intertyp,i,icg)=0.0d0
-              enddo
-            enddo
+          do i=-1,nres
+          do j=1,3
+            gvdwx(j,i)=0.0D0
+            gradx_scp(j,i)=0.0D0
+            gvdwc(j,i)=0.0D0
+            gvdwc_scp(j,i)=0.0D0
+            gvdwc_scpp(j,i)=0.0d0
+            gelc(j,i)=0.0D0
+            gelc_long(j,i)=0.0D0
+            gradb(j,i)=0.0d0
+            gradbx(j,i)=0.0d0
+            gvdwpp(j,i)=0.0d0
+            gel_loc(j,i)=0.0d0
+            gel_loc_long(j,i)=0.0d0
+            ghpbc(j,i)=0.0D0
+            ghpbx(j,i)=0.0D0
+            gcorr3_turn(j,i)=0.0d0
+            gcorr4_turn(j,i)=0.0d0
+            gradcorr(j,i)=0.0d0
+            gradcorr_long(j,i)=0.0d0
+            gradcorr5_long(j,i)=0.0d0
+            gradcorr6_long(j,i)=0.0d0
+            gcorr6_turn_long(j,i)=0.0d0
+            gradcorr5(j,i)=0.0d0
+            gradcorr6(j,i)=0.0d0
+            gcorr6_turn(j,i)=0.0d0
+            gsccorc(j,i)=0.0d0
+            gsccorx(j,i)=0.0d0
+            gradc(j,i,icg)=0.0d0
+            gradx(j,i,icg)=0.0d0
+            gscloc(j,i)=0.0d0
+            gsclocx(j,i)=0.0d0
+            gliptran(j,i)=0.0d0
+            gliptranx(j,i)=0.0d0
+            gliptranc(j,i)=0.0d0
+            gshieldx(j,i)=0.0d0
+            gshieldc(j,i)=0.0d0
+            gshieldc_loc(j,i)=0.0d0
+            gshieldx_ec(j,i)=0.0d0
+            gshieldc_ec(j,i)=0.0d0
+            gshieldc_loc_ec(j,i)=0.0d0
+            gshieldx_t3(j,i)=0.0d0
+            gshieldc_t3(j,i)=0.0d0
+            gshieldc_loc_t3(j,i)=0.0d0
+            gshieldx_t4(j,i)=0.0d0
+            gshieldc_t4(j,i)=0.0d0
+            gshieldc_loc_t4(j,i)=0.0d0
+            gshieldx_ll(j,i)=0.0d0
+            gshieldc_ll(j,i)=0.0d0
+            gshieldc_loc_ll(j,i)=0.0d0
+            gg_tube(j,i)=0.0d0
+            gg_tube_sc(j,i)=0.0d0
+            gradafm(j,i)=0.0d0
+            gradb_nucl(j,i)=0.0d0
+            gradbx_nucl(j,i)=0.0d0
+            gvdwpp_nucl(j,i)=0.0d0
+            gvdwpp(j,i)=0.0d0
+            gelpp(j,i)=0.0d0
+            gvdwpsb(j,i)=0.0d0
+            gvdwpsb1(j,i)=0.0d0
+            gvdwsbc(j,i)=0.0d0
+            gvdwsbx(j,i)=0.0d0
+            gelsbc(j,i)=0.0d0
+            gradcorr_nucl(j,i)=0.0d0
+            gradcorr3_nucl(j,i)=0.0d0
+            gradxorr_nucl(j,i)=0.0d0
+            gradxorr3_nucl(j,i)=0.0d0
+            gelsbx(j,i)=0.0d0
+            gsbloc(j,i)=0.0d0
+            gsblocx(j,i)=0.0d0
+            gradpepcat(j,i)=0.0d0
+            gradpepcatx(j,i)=0.0d0
+            gradcatcat(j,i)=0.0d0
+            gvdwx_scbase(j,i)=0.0d0
+            gvdwc_scbase(j,i)=0.0d0
+            gvdwx_pepbase(j,i)=0.0d0
+            gvdwc_pepbase(j,i)=0.0d0
+            gvdwx_scpho(j,i)=0.0d0
+            gvdwc_scpho(j,i)=0.0d0
+            gvdwc_peppho(j,i)=0.0d0
+            gradnuclcatx(j,i)=0.0d0
+            gradnuclcat(j,i)=0.0d0
+          enddo
+           enddo
+          do i=0,nres
+          do j=1,3
+            do intertyp=1,3
+             gloc_sc(intertyp,i,icg)=0.0d0
             enddo
             enddo
-            do i=1,nres
-             do j=1,maxcontsshi
-             shield_list(j,i)=0
-            do k=1,3
+          enddo
+          enddo
+          do i=1,nres
+           do j=1,maxcontsshi
+           shield_list(j,i)=0
+          do k=1,3
       !C           print *,i,j,k
       !C           print *,i,j,k
-               grad_shield_side(k,j,i)=0.0d0
-               grad_shield_loc(k,j,i)=0.0d0
-             enddo
-             enddo
-             ishield_list(i)=0
-            enddo
+             grad_shield_side(k,j,i)=0.0d0
+             grad_shield_loc(k,j,i)=0.0d0
+           enddo
+           enddo
+           ishield_list(i)=0
+          enddo
 
       !
       ! Initialize the gradient of local energy terms.
 
       !
       ! Initialize the gradient of local energy terms.
@@ -17341,42 +16996,42 @@
       !      allocate(gel_loc_turn4(nres),gel_loc_turn6(nres))  !(maxvar)(maxvar=6*maxres)
       !      allocate(gsccor_loc(nres))      !(maxres)
 
       !      allocate(gel_loc_turn4(nres),gel_loc_turn6(nres))  !(maxvar)(maxvar=6*maxres)
       !      allocate(gsccor_loc(nres))      !(maxres)
 
-            do i=1,4*nres
-            gloc(i,icg)=0.0D0
-            enddo
-            do i=1,nres
-            gel_loc_loc(i)=0.0d0
-            gcorr_loc(i)=0.0d0
-            g_corr5_loc(i)=0.0d0
-            g_corr6_loc(i)=0.0d0
-            gel_loc_turn3(i)=0.0d0
-            gel_loc_turn4(i)=0.0d0
-            gel_loc_turn6(i)=0.0d0
-            gsccor_loc(i)=0.0d0
-            enddo
+          do i=1,4*nres
+          gloc(i,icg)=0.0D0
+          enddo
+          do i=1,nres
+          gel_loc_loc(i)=0.0d0
+          gcorr_loc(i)=0.0d0
+          g_corr5_loc(i)=0.0d0
+          g_corr6_loc(i)=0.0d0
+          gel_loc_turn3(i)=0.0d0
+          gel_loc_turn4(i)=0.0d0
+          gel_loc_turn6(i)=0.0d0
+          gsccor_loc(i)=0.0d0
+          enddo
       ! initialize gcart and gxcart
       !      allocate(gcart(3,0:nres),gxcart(3,0:nres)) !(3,0:MAXRES)
       ! initialize gcart and gxcart
       !      allocate(gcart(3,0:nres),gxcart(3,0:nres)) !(3,0:MAXRES)
-            do i=0,nres
-            do j=1,3
-              gcart(j,i)=0.0d0
-              gxcart(j,i)=0.0d0
-            enddo
-            enddo
-            return
-            end subroutine zerograd
+          do i=0,nres
+          do j=1,3
+            gcart(j,i)=0.0d0
+            gxcart(j,i)=0.0d0
+          enddo
+          enddo
+          return
+          end subroutine zerograd
       !-----------------------------------------------------------------------------
       !-----------------------------------------------------------------------------
-            real(kind=8) function fdum()
-            fdum=0.0D0
-            return
-            end function fdum
+          real(kind=8) function fdum()
+          fdum=0.0D0
+          return
+          end function fdum
       !-----------------------------------------------------------------------------
       ! intcartderiv.F
       !-----------------------------------------------------------------------------
       !-----------------------------------------------------------------------------
       ! intcartderiv.F
       !-----------------------------------------------------------------------------
-            subroutine intcartderiv
+          subroutine intcartderiv
       !      implicit real*8 (a-h,o-z)
       !      include 'DIMENSIONS'
 #ifdef MPI
       !      implicit real*8 (a-h,o-z)
       !      include 'DIMENSIONS'
 #ifdef MPI
-            include 'mpif.h'
+          include 'mpif.h'
 #endif
       !      include 'COMMON.SETUP'
       !      include 'COMMON.CHAIN' 
 #endif
       !      include 'COMMON.SETUP'
       !      include 'COMMON.CHAIN' 
@@ -17387,19 +17042,19 @@
       !      include 'COMMON.IOUNITS'
       !      include 'COMMON.LOCAL'
       !      include 'COMMON.SCCOR'
       !      include 'COMMON.IOUNITS'
       !      include 'COMMON.LOCAL'
       !      include 'COMMON.SCCOR'
-            real(kind=8) :: pi4,pi34
-            real(kind=8),dimension(3,2,nres) :: dcostheta ! (3,2,maxres)
-            real(kind=8),dimension(3,3,nres) :: dcosphi,dsinphi,dcosalpha,&
-                      dcosomega,dsinomega !(3,3,maxres)
-            real(kind=8),dimension(3) :: vo1,vo2,vo3,dummy,vp1,vp2,vp3,vpp1,n
-          
-            integer :: i,j,k
-            real(kind=8) :: cost,sint,cost1,sint1,cost2,sint2,sing,cosg,scalp,&
-                    fac0,fac1,fac2,fac3,fac4,fac5,fac6,ctgt,ctgt1,cosg_inv,&
-                    fac7,fac8,fac9,scala1,scala2,cosa,sina,sino,fac15,fac16,&
-                    fac17,coso_inv,fac10,fac11,fac12,fac13,fac14
-            integer :: nres2
-            nres2=2*nres
+          real(kind=8) :: pi4,pi34
+          real(kind=8),dimension(3,2,nres) :: dcostheta ! (3,2,maxres)
+          real(kind=8),dimension(3,3,nres) :: dcosphi,dsinphi,dcosalpha,&
+                  dcosomega,dsinomega !(3,3,maxres)
+          real(kind=8),dimension(3) :: vo1,vo2,vo3,dummy,vp1,vp2,vp3,vpp1,n
+        
+          integer :: i,j,k
+          real(kind=8) :: cost,sint,cost1,sint1,cost2,sint2,sing,cosg,scalp,&
+                fac0,fac1,fac2,fac3,fac4,fac5,fac6,ctgt,ctgt1,cosg_inv,&
+                fac7,fac8,fac9,scala1,scala2,cosa,sina,sino,fac15,fac16,&
+                fac17,coso_inv,fac10,fac11,fac12,fac13,fac14,IERROR
+          integer :: nres2
+          nres2=2*nres
 
       !el from module energy-------------
       !el      allocate(dcostau(3,3,3,itau_start:itau_end)) !(3,3,3,maxres2)maxres2=2*maxres
 
       !el from module energy-------------
       !el      allocate(dcostau(3,3,3,itau_start:itau_end)) !(3,3,3,maxres2)maxres2=2*maxres
@@ -17415,541 +17070,608 @@
 
 
 #if defined(MPI) && defined(PARINTDER)
 
 
 #if defined(MPI) && defined(PARINTDER)
-            if (nfgtasks.gt.1 .and. me.eq.king) &
-            call MPI_Bcast(8,1,MPI_INTEGER,king,FG_COMM,IERROR)
+          if (nfgtasks.gt.1 .and. me.eq.king) &
+          call MPI_Bcast(8,1,MPI_INTEGER,king,FG_COMM,IERROR)
 #endif
 #endif
-            pi4 = 0.5d0*pipol
-            pi34 = 3*pi4
+          pi4 = 0.5d0*pipol
+          pi34 = 3*pi4
 
       !      allocate(dtheta(3,2,nres))      !(3,2,maxres)
       !      allocate(dphi(3,3,nres),dalpha(3,3,nres),domega(3,3,nres)) !(3,3,maxres)
 
       !     write (iout,*) "iphi1_start",iphi1_start," iphi1_end",iphi1_end
 
       !      allocate(dtheta(3,2,nres))      !(3,2,maxres)
       !      allocate(dphi(3,3,nres),dalpha(3,3,nres),domega(3,3,nres)) !(3,3,maxres)
 
       !     write (iout,*) "iphi1_start",iphi1_start," iphi1_end",iphi1_end
-            do i=1,nres
-            do j=1,3
-              dtheta(j,1,i)=0.0d0
-              dtheta(j,2,i)=0.0d0
-              dphi(j,1,i)=0.0d0
-              dphi(j,2,i)=0.0d0
-              dphi(j,3,i)=0.0d0
-            enddo
-            enddo
+          do i=1,nres
+          do j=1,3
+            dtheta(j,1,i)=0.0d0
+            dtheta(j,2,i)=0.0d0
+            dphi(j,1,i)=0.0d0
+            dphi(j,2,i)=0.0d0
+            dphi(j,3,i)=0.0d0
+            dcosomicron(j,1,1,i)=0.0d0
+            dcosomicron(j,1,2,i)=0.0d0
+            dcosomicron(j,2,1,i)=0.0d0
+            dcosomicron(j,2,2,i)=0.0d0
+          enddo
+          enddo
       ! Derivatives of theta's
 #if defined(MPI) && defined(PARINTDER)
       ! We need dtheta(:,:,i-1) to compute dphi(:,:,i)
       ! Derivatives of theta's
 #if defined(MPI) && defined(PARINTDER)
       ! We need dtheta(:,:,i-1) to compute dphi(:,:,i)
-            do i=max0(ithet_start-1,3),ithet_end
+          do i=max0(ithet_start-1,3),ithet_end
 #else
 #else
-            do i=3,nres
+          do i=3,nres
 #endif
 #endif
-            cost=dcos(theta(i))
-            sint=sqrt(1-cost*cost)
-            do j=1,3
-              dcostheta(j,1,i)=-(dc_norm(j,i-1)+cost*dc_norm(j,i-2))/&
-              vbld(i-1)
-              if (itype(i-1,1).ne.ntyp1) dtheta(j,1,i)=-dcostheta(j,1,i)/sint
-              dcostheta(j,2,i)=-(dc_norm(j,i-2)+cost*dc_norm(j,i-1))/&
-              vbld(i)
-              if (itype(i-1,1).ne.ntyp1) dtheta(j,2,i)=-dcostheta(j,2,i)/sint
-            enddo
-            enddo
+          cost=dcos(theta(i))
+          sint=sqrt(1-cost*cost)
+          do j=1,3
+            dcostheta(j,1,i)=-(dc_norm(j,i-1)+cost*dc_norm(j,i-2))/&
+            vbld(i-1)
+            if (((itype(i-1,1).ne.ntyp1).and.(sint.ne.0.0d0))) &
+             dtheta(j,1,i)=-dcostheta(j,1,i)/sint
+            dcostheta(j,2,i)=-(dc_norm(j,i-2)+cost*dc_norm(j,i-1))/&
+            vbld(i)
+            if ((itype(i-1,1).ne.ntyp1).and.(sint.ne.0.0d0))&
+             dtheta(j,2,i)=-dcostheta(j,2,i)/sint
+          enddo
+          enddo
 #if defined(MPI) && defined(PARINTDER)
       ! We need dtheta(:,:,i-1) to compute dphi(:,:,i)
 #if defined(MPI) && defined(PARINTDER)
       ! We need dtheta(:,:,i-1) to compute dphi(:,:,i)
-            do i=max0(ithet_start-1,3),ithet_end
+          do i=max0(ithet_start-1,3),ithet_end
 #else
 #else
-            do i=3,nres
+          do i=3,nres
 #endif
 #endif
-            if ((itype(i-1,1).ne.10).and.(itype(i-1,1).ne.ntyp1)) then
-            cost1=dcos(omicron(1,i))
-            sint1=sqrt(1-cost1*cost1)
-            cost2=dcos(omicron(2,i))
-            sint2=sqrt(1-cost2*cost2)
-             do j=1,3
+          if ((itype(i-1,1).ne.10).and.(itype(i-1,1).ne.ntyp1).and.molnum(i).ne.5) then
+          cost1=dcos(omicron(1,i))
+          sint1=sqrt(1-cost1*cost1)
+          cost2=dcos(omicron(2,i))
+          sint2=sqrt(1-cost2*cost2)
+           do j=1,3
       !C Calculate derivative over first omicron (Cai-2,Cai-1,SCi-1) 
       !C Calculate derivative over first omicron (Cai-2,Cai-1,SCi-1) 
-              dcosomicron(j,1,1,i)=-(dc_norm(j,i-1+nres)+ &
-              cost1*dc_norm(j,i-2))/ &
-              vbld(i-1)
-              domicron(j,1,1,i)=-1.0/sint1*dcosomicron(j,1,1,i)
-              dcosomicron(j,1,2,i)=-(dc_norm(j,i-2) &
-              +cost1*(dc_norm(j,i-1+nres)))/ &
-              vbld(i-1+nres)
-              domicron(j,1,2,i)=-1.0/sint1*dcosomicron(j,1,2,i)
+            dcosomicron(j,1,1,i)=-(dc_norm(j,i-1+nres)+ &
+            cost1*dc_norm(j,i-2))/ &
+            vbld(i-1)
+            domicron(j,1,1,i)=-1.0/sint1*dcosomicron(j,1,1,i)
+            dcosomicron(j,1,2,i)=-(dc_norm(j,i-2) &
+            +cost1*(dc_norm(j,i-1+nres)))/ &
+            vbld(i-1+nres)
+            domicron(j,1,2,i)=-1.0/sint1*dcosomicron(j,1,2,i)
       !C Calculate derivative over second omicron Sci-1,Cai-1 Cai
       !C Looks messy but better than if in loop
       !C Calculate derivative over second omicron Sci-1,Cai-1 Cai
       !C Looks messy but better than if in loop
-              dcosomicron(j,2,1,i)=-(-dc_norm(j,i-1+nres) &
-              +cost2*dc_norm(j,i-1))/ &
-              vbld(i)
-              domicron(j,2,1,i)=-1.0/sint2*dcosomicron(j,2,1,i)
-              dcosomicron(j,2,2,i)=-(dc_norm(j,i-1) &
-               +cost2*(-dc_norm(j,i-1+nres)))/ &
-              vbld(i-1+nres)
+            dcosomicron(j,2,1,i)=-(-dc_norm(j,i-1+nres) &
+            +cost2*dc_norm(j,i-1))/ &
+            vbld(i)
+            domicron(j,2,1,i)=-1.0/sint2*dcosomicron(j,2,1,i)
+            dcosomicron(j,2,2,i)=-(dc_norm(j,i-1) &
+             +cost2*(-dc_norm(j,i-1+nres)))/ &
+            vbld(i-1+nres)
       !          write(iout,*) "vbld", i,itype(i,1),vbld(i-1+nres)
       !          write(iout,*) "vbld", i,itype(i,1),vbld(i-1+nres)
-              domicron(j,2,2,i)=-1.0/sint2*dcosomicron(j,2,2,i)
-            enddo
-             endif
-            enddo
+            domicron(j,2,2,i)=-1.0/sint2*dcosomicron(j,2,2,i)
+          enddo
+           endif
+          enddo
       !elwrite(iout,*) "after vbld write"
       ! Derivatives of phi:
       ! If phi is 0 or 180 degrees, then the formulas 
       ! have to be derived by power series expansion of the
       ! conventional formulas around 0 and 180.
 #ifdef PARINTDER
       !elwrite(iout,*) "after vbld write"
       ! Derivatives of phi:
       ! If phi is 0 or 180 degrees, then the formulas 
       ! have to be derived by power series expansion of the
       ! conventional formulas around 0 and 180.
 #ifdef PARINTDER
-            do i=iphi1_start,iphi1_end
+          do i=iphi1_start,iphi1_end
 #else
 #else
-            do i=4,nres      
+          do i=4,nres      
 #endif
       !        if (itype(i-1,1).eq.21 .or. itype(i-2,1).eq.21 ) cycle
       ! the conventional case
 #endif
       !        if (itype(i-1,1).eq.21 .or. itype(i-2,1).eq.21 ) cycle
       ! the conventional case
-            sint=dsin(theta(i))
-            sint1=dsin(theta(i-1))
-            sing=dsin(phi(i))
-            cost=dcos(theta(i))
-            cost1=dcos(theta(i-1))
-            cosg=dcos(phi(i))
-            scalp=scalar(dc_norm(1,i-3),dc_norm(1,i-1))
-            fac0=1.0d0/(sint1*sint)
-            fac1=cost*fac0
-            fac2=cost1*fac0
-            fac3=cosg*cost1/(sint1*sint1)
-            fac4=cosg*cost/(sint*sint)
+          sint=dsin(theta(i))
+          sint1=dsin(theta(i-1))
+          sing=dsin(phi(i))
+          cost=dcos(theta(i))
+          cost1=dcos(theta(i-1))
+          cosg=dcos(phi(i))
+          scalp=scalar(dc_norm(1,i-3),dc_norm(1,i-1))
+          if ((sint*sint1).eq.0.0d0) then
+          fac0=0.0d0
+          else
+          fac0=1.0d0/(sint1*sint)
+          endif
+          fac1=cost*fac0
+          fac2=cost1*fac0
+          if (sint1.ne.0.0d0) then
+          fac3=cosg*cost1/(sint1*sint1)
+          else
+          fac3=0.0d0
+          endif
+          if (sint.ne.0.0d0) then
+          fac4=cosg*cost/(sint*sint)
+          else
+          fac4=0.0d0
+          endif
       !    Obtaining the gamma derivatives from sine derivative                           
       !    Obtaining the gamma derivatives from sine derivative                           
-             if (phi(i).gt.-pi4.and.phi(i).le.pi4.or. &
-               phi(i).gt.pi34.and.phi(i).le.pi.or. &
-               phi(i).ge.-pi.and.phi(i).le.-pi34) then
-             call vecpr(dc_norm(1,i-1),dc_norm(1,i-2),vp1)
-             call vecpr(dc_norm(1,i-3),dc_norm(1,i-1),vp2)
-             call vecpr(dc_norm(1,i-3),dc_norm(1,i-2),vp3) 
-             do j=1,3
-                ctgt=cost/sint
-                ctgt1=cost1/sint1
-                cosg_inv=1.0d0/cosg
-                if (itype(i-1,1).ne.ntyp1 .and. itype(i-2,1).ne.ntyp1) then
-                dsinphi(j,1,i)=-sing*ctgt1*dtheta(j,1,i-1) &
-                  -(fac0*vp1(j)+sing*dc_norm(j,i-3))*vbld_inv(i-2)
-                dphi(j,1,i)=cosg_inv*dsinphi(j,1,i)
-                dsinphi(j,2,i)= &
-                  -sing*(ctgt1*dtheta(j,2,i-1)+ctgt*dtheta(j,1,i)) &
-                  -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1)
-                dphi(j,2,i)=cosg_inv*dsinphi(j,2,i)
-                dsinphi(j,3,i)=-sing*ctgt*dtheta(j,2,i) &
-                  +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i)
+           if (phi(i).gt.-pi4.and.phi(i).le.pi4.or. &
+             phi(i).gt.pi34.and.phi(i).le.pi.or. &
+             phi(i).ge.-pi.and.phi(i).le.-pi34) then
+           call vecpr(dc_norm(1,i-1),dc_norm(1,i-2),vp1)
+           call vecpr(dc_norm(1,i-3),dc_norm(1,i-1),vp2)
+           call vecpr(dc_norm(1,i-3),dc_norm(1,i-2),vp3) 
+           do j=1,3
+            if (sint.ne.0.0d0) then
+            ctgt=cost/sint
+            else
+            ctgt=0.0d0
+            endif
+            if (sint1.ne.0.0d0) then
+            ctgt1=cost1/sint1
+            else
+            ctgt1=0.0d0
+            endif
+            cosg_inv=1.0d0/cosg
+            if (itype(i-1,1).ne.ntyp1 .and. itype(i-2,1).ne.ntyp1) then
+            dsinphi(j,1,i)=-sing*ctgt1*dtheta(j,1,i-1) &
+              -(fac0*vp1(j)+sing*dc_norm(j,i-3))*vbld_inv(i-2)
+            dphi(j,1,i)=cosg_inv*dsinphi(j,1,i)
+            dsinphi(j,2,i)= &
+              -sing*(ctgt1*dtheta(j,2,i-1)+ctgt*dtheta(j,1,i)) &
+              -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1)
+            dphi(j,2,i)=cosg_inv*dsinphi(j,2,i)
+            dsinphi(j,3,i)=-sing*ctgt*dtheta(j,2,i) &
+              +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i)
       !     &        +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1)
       !     &        +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1)
-                dphi(j,3,i)=cosg_inv*dsinphi(j,3,i)
-                endif
+            dphi(j,3,i)=cosg_inv*dsinphi(j,3,i)
+            endif
+!             write(iout,*) "just after,close to pi",dphi(j,3,i),&
+!              sing*(ctgt1*dtheta(j,2,i-1)),ctgt*dtheta(j,1,i), &
+!              (fac0*vp2(j)+sing*dc_norm(j,i-2)),vbld_inv(i-1)
+
       ! Bug fixed 3/24/05 (AL)
       ! Bug fixed 3/24/05 (AL)
-             enddo                                                        
+           enddo                                                        
       !   Obtaining the gamma derivatives from cosine derivative
       !   Obtaining the gamma derivatives from cosine derivative
-            else
-               do j=1,3
-               if (itype(i-1,1).ne.ntyp1 .and. itype(i-2,1).ne.ntyp1) then
-               dcosphi(j,1,i)=fac1*dcostheta(j,1,i-1)+fac3* &
-               dcostheta(j,1,i-1)-fac0*(dc_norm(j,i-1)-scalp* &
-               dc_norm(j,i-3))/vbld(i-2)
-               dphi(j,1,i)=-1.0/sing*dcosphi(j,1,i)       
-               dcosphi(j,2,i)=fac1*dcostheta(j,2,i-1)+fac2* &
-               dcostheta(j,1,i)+fac3*dcostheta(j,2,i-1)+fac4* &
-               dcostheta(j,1,i)
-               dphi(j,2,i)=-1.0/sing*dcosphi(j,2,i)      
-               dcosphi(j,3,i)=fac2*dcostheta(j,2,i)+fac4* &
-               dcostheta(j,2,i)-fac0*(dc_norm(j,i-3)-scalp* &
-               dc_norm(j,i-1))/vbld(i)
-               dphi(j,3,i)=-1.0/sing*dcosphi(j,3,i)       
+          else
+             do j=1,3
+             if (itype(i-1,1).ne.ntyp1 .and. itype(i-2,1).ne.ntyp1) then
+             dcosphi(j,1,i)=fac1*dcostheta(j,1,i-1)+fac3* &
+             dcostheta(j,1,i-1)-fac0*(dc_norm(j,i-1)-scalp* &
+             dc_norm(j,i-3))/vbld(i-2)
+             dphi(j,1,i)=-1.0/sing*dcosphi(j,1,i)       
+             dcosphi(j,2,i)=fac1*dcostheta(j,2,i-1)+fac2* &
+             dcostheta(j,1,i)+fac3*dcostheta(j,2,i-1)+fac4* &
+             dcostheta(j,1,i)
+             dphi(j,2,i)=-1.0/sing*dcosphi(j,2,i)      
+             dcosphi(j,3,i)=fac2*dcostheta(j,2,i)+fac4* &
+             dcostheta(j,2,i)-fac0*(dc_norm(j,i-3)-scalp* &
+             dc_norm(j,i-1))/vbld(i)
+             dphi(j,3,i)=-1.0/sing*dcosphi(j,3,i)       
 !#define DEBUG
 #ifdef DEBUG
 !#define DEBUG
 #ifdef DEBUG
-               write(iout,*) "just after",dphi(j,3,i),sing,dcosphi(j,3,i)
+             write(iout,*) "just after",dphi(j,3,i),sing,dcosphi(j,3,i)
 #endif
 !#undef DEBUG
 #endif
 !#undef DEBUG
-               endif
-             enddo
-            endif                                                                                                         
-            enddo
+             endif
+           enddo
+          endif                                                                                                         
+          enddo
       !alculate derivative of Tauangle
 #ifdef PARINTDER
       !alculate derivative of Tauangle
 #ifdef PARINTDER
-            do i=itau_start,itau_end
+          do i=itau_start,itau_end
 #else
 #else
-            do i=3,nres
+          do i=3,nres
       !elwrite(iout,*) " vecpr",i,nres
 #endif
       !elwrite(iout,*) " vecpr",i,nres
 #endif
-             if ((itype(i-2,1).eq.ntyp1).or.(itype(i-2,1).eq.10)) cycle
+           if ((itype(i-2,1).eq.ntyp1).or.(itype(i-2,1).eq.10)) cycle
       !       if ((itype(i-2,1).eq.ntyp1).or.(itype(i-2,1).eq.10).or.
       !     &     (itype(i-1,1).eq.ntyp1).or.(itype(i,1).eq.ntyp1)) cycle
       !c dtauangle(j,intertyp,dervityp,residue number)
       !c INTERTYP=1 SC...Ca...Ca..Ca
       ! the conventional case
       !       if ((itype(i-2,1).eq.ntyp1).or.(itype(i-2,1).eq.10).or.
       !     &     (itype(i-1,1).eq.ntyp1).or.(itype(i,1).eq.ntyp1)) cycle
       !c dtauangle(j,intertyp,dervityp,residue number)
       !c INTERTYP=1 SC...Ca...Ca..Ca
       ! the conventional case
-            sint=dsin(theta(i))
-            sint1=dsin(omicron(2,i-1))
-            sing=dsin(tauangle(1,i))
-            cost=dcos(theta(i))
-            cost1=dcos(omicron(2,i-1))
-            cosg=dcos(tauangle(1,i))
+          sint=dsin(theta(i))
+          sint1=dsin(omicron(2,i-1))
+          sing=dsin(tauangle(1,i))
+          cost=dcos(theta(i))
+          cost1=dcos(omicron(2,i-1))
+          cosg=dcos(tauangle(1,i))
       !elwrite(iout,*) " vecpr5",i,nres
       !elwrite(iout,*) " vecpr5",i,nres
-            do j=1,3
+          do j=1,3
       !elwrite(iout,*) " vecpreee",i,nres,j,i-2+nres
       !elwrite(iout,*) " vecpr5",dc_norm2(1,1)
       !elwrite(iout,*) " vecpreee",i,nres,j,i-2+nres
       !elwrite(iout,*) " vecpr5",dc_norm2(1,1)
-            dc_norm2(j,i-2+nres)=-dc_norm(j,i-2+nres)
+          dc_norm2(j,i-2+nres)=-dc_norm(j,i-2+nres)
       !       write(iout,*) dc_norm2(j,i-2+nres),"dcnorm"
       !       write(iout,*) dc_norm2(j,i-2+nres),"dcnorm"
-            enddo
-            scalp=scalar(dc_norm2(1,i-2+nres),dc_norm(1,i-1))
-            fac0=1.0d0/(sint1*sint)
-            fac1=cost*fac0
-            fac2=cost1*fac0
-            fac3=cosg*cost1/(sint1*sint1)
-            fac4=cosg*cost/(sint*sint)
-      !        write(iout,*) "faki",fac0,fac1,fac2,fac3,fac4
+          enddo
+          scalp=scalar(dc_norm2(1,i-2+nres),dc_norm(1,i-1))
+      !        write(iout,*) "faki",fac0,fac1,fac2,fac3,fac
+        if ((sint*sint1).eq.0.0d0) then
+          fac0=0.0d0
+          else
+          fac0=1.0d0/(sint1*sint)
+          endif
+          fac1=cost*fac0
+          fac2=cost1*fac0
+          if (sint1.ne.0.0d0) then
+          fac3=cosg*cost1/(sint1*sint1)
+          else
+          fac3=0.0d0
+          endif
+          if (sint.ne.0.0d0) then
+          fac4=cosg*cost/(sint*sint)
+          else
+          fac4=0.0d0
+          endif
+
       !    Obtaining the gamma derivatives from sine derivative                                
       !    Obtaining the gamma derivatives from sine derivative                                
-             if (tauangle(1,i).gt.-pi4.and.tauangle(1,i).le.pi4.or. &
-               tauangle(1,i).gt.pi34.and.tauangle(1,i).le.pi.or. &
-               tauangle(1,i).gt.-pi.and.tauangle(1,i).le.-pi34) then
-             call vecpr(dc_norm(1,i-1),dc_norm(1,i-2),vp1)
-             call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-1),vp2)
-             call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-2),vp3)
-            do j=1,3
-                ctgt=cost/sint
-                ctgt1=cost1/sint1
-                cosg_inv=1.0d0/cosg
-                dsintau(j,1,1,i)=-sing*ctgt1*domicron(j,2,2,i-1) &
-             -(fac0*vp1(j)+sing*(dc_norm2(j,i-2+nres))) &
-             *vbld_inv(i-2+nres)
-                dtauangle(j,1,1,i)=cosg_inv*dsintau(j,1,1,i)
-                dsintau(j,1,2,i)= &
-                  -sing*(ctgt1*domicron(j,2,1,i-1)+ctgt*dtheta(j,1,i)) &
-                  -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1)
+           if (tauangle(1,i).gt.-pi4.and.tauangle(1,i).le.pi4.or. &
+             tauangle(1,i).gt.pi34.and.tauangle(1,i).le.pi.or. &
+             tauangle(1,i).gt.-pi.and.tauangle(1,i).le.-pi34) then
+           call vecpr(dc_norm(1,i-1),dc_norm(1,i-2),vp1)
+           call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-1),vp2)
+           call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-2),vp3)
+          do j=1,3
+            ctgt=cost/sint
+            ctgt1=cost1/sint1
+            cosg_inv=1.0d0/cosg
+            dsintau(j,1,1,i)=-sing*ctgt1*domicron(j,2,2,i-1) &
+           -(fac0*vp1(j)+sing*(dc_norm2(j,i-2+nres))) &
+           *vbld_inv(i-2+nres)
+            dtauangle(j,1,1,i)=cosg_inv*dsintau(j,1,1,i)
+            dsintau(j,1,2,i)= &
+              -sing*(ctgt1*domicron(j,2,1,i-1)+ctgt*dtheta(j,1,i)) &
+              -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1)
       !            write(iout,*) "dsintau", dsintau(j,1,2,i)
       !            write(iout,*) "dsintau", dsintau(j,1,2,i)
-                dtauangle(j,1,2,i)=cosg_inv*dsintau(j,1,2,i)
+            dtauangle(j,1,2,i)=cosg_inv*dsintau(j,1,2,i)
       ! Bug fixed 3/24/05 (AL)
       ! Bug fixed 3/24/05 (AL)
-                dsintau(j,1,3,i)=-sing*ctgt*dtheta(j,2,i) &
-                  +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i)
+            dsintau(j,1,3,i)=-sing*ctgt*dtheta(j,2,i) &
+              +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i)
       !     &        +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1)
       !     &        +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1)
-                dtauangle(j,1,3,i)=cosg_inv*dsintau(j,1,3,i)
-             enddo
+            dtauangle(j,1,3,i)=cosg_inv*dsintau(j,1,3,i)
+           enddo
       !   Obtaining the gamma derivatives from cosine derivative
       !   Obtaining the gamma derivatives from cosine derivative
-            else
-               do j=1,3
-               dcostau(j,1,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3* &
-               dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1)-scalp* &
-               (dc_norm2(j,i-2+nres)))/vbld(i-2+nres)
-               dtauangle(j,1,1,i)=-1/sing*dcostau(j,1,1,i)
-               dcostau(j,1,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2* &
-               dcostheta(j,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4* &
-               dcostheta(j,1,i)
-               dtauangle(j,1,2,i)=-1/sing*dcostau(j,1,2,i)
-               dcostau(j,1,3,i)=fac2*dcostheta(j,2,i)+fac4* &
-               dcostheta(j,2,i)-fac0*(-dc_norm(j,i-2+nres)-scalp* &
-               dc_norm(j,i-1))/vbld(i)
-               dtauangle(j,1,3,i)=-1/sing*dcostau(j,1,3,i)
+          else
+             do j=1,3
+             dcostau(j,1,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3* &
+             dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1)-scalp* &
+             (dc_norm2(j,i-2+nres)))/vbld(i-2+nres)
+             dtauangle(j,1,1,i)=-1/sing*dcostau(j,1,1,i)
+             dcostau(j,1,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2* &
+             dcostheta(j,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4* &
+             dcostheta(j,1,i)
+             dtauangle(j,1,2,i)=-1/sing*dcostau(j,1,2,i)
+             dcostau(j,1,3,i)=fac2*dcostheta(j,2,i)+fac4* &
+             dcostheta(j,2,i)-fac0*(-dc_norm(j,i-2+nres)-scalp* &
+             dc_norm(j,i-1))/vbld(i)
+             dtauangle(j,1,3,i)=-1/sing*dcostau(j,1,3,i)
       !         write (iout,*) "else",i
       !         write (iout,*) "else",i
-             enddo
-            endif
+           enddo
+          endif
       !        do k=1,3                 
       !        write(iout,*) "tu",i,k,(dtauangle(j,1,k,i),j=1,3)        
       !        enddo                
       !        do k=1,3                 
       !        write(iout,*) "tu",i,k,(dtauangle(j,1,k,i),j=1,3)        
       !        enddo                
-            enddo
+          enddo
       !C Second case Ca...Ca...Ca...SC
 #ifdef PARINTDER
       !C Second case Ca...Ca...Ca...SC
 #ifdef PARINTDER
-            do i=itau_start,itau_end
+          do i=itau_start,itau_end
 #else
 #else
-            do i=4,nres
+          do i=4,nres
 #endif
 #endif
-             if ((itype(i-1,1).eq.ntyp1).or.(itype(i-1,1).eq.10).or. &
-              (itype(i-2,1).eq.ntyp1).or.(itype(i-3,1).eq.ntyp1)) cycle
+           if ((itype(i-1,1).eq.ntyp1).or.(itype(i-1,1).eq.10).or. &
+            (itype(i-2,1).eq.ntyp1).or.(itype(i-3,1).eq.ntyp1)) cycle
       ! the conventional case
       ! the conventional case
-            sint=dsin(omicron(1,i))
-            sint1=dsin(theta(i-1))
-            sing=dsin(tauangle(2,i))
-            cost=dcos(omicron(1,i))
-            cost1=dcos(theta(i-1))
-            cosg=dcos(tauangle(2,i))
+          sint=dsin(omicron(1,i))
+          sint1=dsin(theta(i-1))
+          sing=dsin(tauangle(2,i))
+          cost=dcos(omicron(1,i))
+          cost1=dcos(theta(i-1))
+          cosg=dcos(tauangle(2,i))
       !        do j=1,3
       !        dc_norm2(j,i-1+nres)=-dc_norm(j,i-1+nres)
       !        enddo
       !        do j=1,3
       !        dc_norm2(j,i-1+nres)=-dc_norm(j,i-1+nres)
       !        enddo
-            scalp=scalar(dc_norm(1,i-3),dc_norm(1,i-1+nres))
-            fac0=1.0d0/(sint1*sint)
-            fac1=cost*fac0
-            fac2=cost1*fac0
-            fac3=cosg*cost1/(sint1*sint1)
-            fac4=cosg*cost/(sint*sint)
+          scalp=scalar(dc_norm(1,i-3),dc_norm(1,i-1+nres))
+        if ((sint*sint1).eq.0.0d0) then
+          fac0=0.0d0
+          else
+          fac0=1.0d0/(sint1*sint)
+          endif
+          fac1=cost*fac0
+          fac2=cost1*fac0
+          if (sint1.ne.0.0d0) then
+          fac3=cosg*cost1/(sint1*sint1)
+          else
+          fac3=0.0d0
+          endif
+          if (sint.ne.0.0d0) then
+          fac4=cosg*cost/(sint*sint)
+          else
+          fac4=0.0d0
+          endif
       !    Obtaining the gamma derivatives from sine derivative                                
       !    Obtaining the gamma derivatives from sine derivative                                
-             if (tauangle(2,i).gt.-pi4.and.tauangle(2,i).le.pi4.or. &
-               tauangle(2,i).gt.pi34.and.tauangle(2,i).le.pi.or. &
-               tauangle(2,i).gt.-pi.and.tauangle(2,i).le.-pi34) then
-             call vecpr(dc_norm2(1,i-1+nres),dc_norm(1,i-2),vp1)
-             call vecpr(dc_norm(1,i-3),dc_norm(1,i-1+nres),vp2)
-             call vecpr(dc_norm(1,i-3),dc_norm(1,i-2),vp3)
-            do j=1,3
-                ctgt=cost/sint
-                ctgt1=cost1/sint1
-                cosg_inv=1.0d0/cosg
-                dsintau(j,2,1,i)=-sing*ctgt1*dtheta(j,1,i-1) &
-                  +(fac0*vp1(j)-sing*dc_norm(j,i-3))*vbld_inv(i-2)
+           if (tauangle(2,i).gt.-pi4.and.tauangle(2,i).le.pi4.or. &
+             tauangle(2,i).gt.pi34.and.tauangle(2,i).le.pi.or. &
+             tauangle(2,i).gt.-pi.and.tauangle(2,i).le.-pi34) then
+           call vecpr(dc_norm2(1,i-1+nres),dc_norm(1,i-2),vp1)
+           call vecpr(dc_norm(1,i-3),dc_norm(1,i-1+nres),vp2)
+           call vecpr(dc_norm(1,i-3),dc_norm(1,i-2),vp3)
+          do j=1,3
+            ctgt=cost/sint
+            ctgt1=cost1/sint1
+            cosg_inv=1.0d0/cosg
+            dsintau(j,2,1,i)=-sing*ctgt1*dtheta(j,1,i-1) &
+              +(fac0*vp1(j)-sing*dc_norm(j,i-3))*vbld_inv(i-2)
       !       write(iout,*) i,j,dsintau(j,2,1,i),sing*ctgt1*dtheta(j,1,i-1),
       !     &fac0*vp1(j),sing*dc_norm(j,i-3),vbld_inv(i-2),"dsintau(2,1)"
       !       write(iout,*) i,j,dsintau(j,2,1,i),sing*ctgt1*dtheta(j,1,i-1),
       !     &fac0*vp1(j),sing*dc_norm(j,i-3),vbld_inv(i-2),"dsintau(2,1)"
-                dtauangle(j,2,1,i)=cosg_inv*dsintau(j,2,1,i)
-                dsintau(j,2,2,i)= &
-                  -sing*(ctgt1*dtheta(j,2,i-1)+ctgt*domicron(j,1,1,i)) &
-                  -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1)
+            dtauangle(j,2,1,i)=cosg_inv*dsintau(j,2,1,i)
+            dsintau(j,2,2,i)= &
+              -sing*(ctgt1*dtheta(j,2,i-1)+ctgt*domicron(j,1,1,i)) &
+              -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1)
       !            write(iout,*) "sprawdzenie",i,j,sing*ctgt1*dtheta(j,2,i-1),
       !     & sing*ctgt*domicron(j,1,2,i),
       !     & (fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1)
       !            write(iout,*) "sprawdzenie",i,j,sing*ctgt1*dtheta(j,2,i-1),
       !     & sing*ctgt*domicron(j,1,2,i),
       !     & (fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1)
-                dtauangle(j,2,2,i)=cosg_inv*dsintau(j,2,2,i)
+            dtauangle(j,2,2,i)=cosg_inv*dsintau(j,2,2,i)
       ! Bug fixed 3/24/05 (AL)
       ! Bug fixed 3/24/05 (AL)
-                dsintau(j,2,3,i)=-sing*ctgt*domicron(j,1,2,i) &
-                 +(fac0*vp3(j)-sing*dc_norm(j,i-1+nres))*vbld_inv(i-1+nres)
+            dsintau(j,2,3,i)=-sing*ctgt*domicron(j,1,2,i) &
+             +(fac0*vp3(j)-sing*dc_norm(j,i-1+nres))*vbld_inv(i-1+nres)
       !     &        +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1)
       !     &        +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1)
-                dtauangle(j,2,3,i)=cosg_inv*dsintau(j,2,3,i)
-             enddo
+            dtauangle(j,2,3,i)=cosg_inv*dsintau(j,2,3,i)
+           enddo
       !   Obtaining the gamma derivatives from cosine derivative
       !   Obtaining the gamma derivatives from cosine derivative
-            else
-               do j=1,3
-               dcostau(j,2,1,i)=fac1*dcostheta(j,1,i-1)+fac3* &
-               dcostheta(j,1,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp* &
-               dc_norm(j,i-3))/vbld(i-2)
-               dtauangle(j,2,1,i)=-1/sing*dcostau(j,2,1,i)
-               dcostau(j,2,2,i)=fac1*dcostheta(j,2,i-1)+fac2* &
-               dcosomicron(j,1,1,i)+fac3*dcostheta(j,2,i-1)+fac4* &
-               dcosomicron(j,1,1,i)
-               dtauangle(j,2,2,i)=-1/sing*dcostau(j,2,2,i)
-               dcostau(j,2,3,i)=fac2*dcosomicron(j,1,2,i)+fac4* &
-               dcosomicron(j,1,2,i)-fac0*(dc_norm(j,i-3)-scalp* &
-               dc_norm(j,i-1+nres))/vbld(i-1+nres)
-               dtauangle(j,2,3,i)=-1/sing*dcostau(j,2,3,i)
+          else
+             do j=1,3
+             dcostau(j,2,1,i)=fac1*dcostheta(j,1,i-1)+fac3* &
+             dcostheta(j,1,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp* &
+             dc_norm(j,i-3))/vbld(i-2)
+             dtauangle(j,2,1,i)=-1/sing*dcostau(j,2,1,i)
+             dcostau(j,2,2,i)=fac1*dcostheta(j,2,i-1)+fac2* &
+             dcosomicron(j,1,1,i)+fac3*dcostheta(j,2,i-1)+fac4* &
+             dcosomicron(j,1,1,i)
+             dtauangle(j,2,2,i)=-1/sing*dcostau(j,2,2,i)
+             dcostau(j,2,3,i)=fac2*dcosomicron(j,1,2,i)+fac4* &
+             dcosomicron(j,1,2,i)-fac0*(dc_norm(j,i-3)-scalp* &
+             dc_norm(j,i-1+nres))/vbld(i-1+nres)
+             dtauangle(j,2,3,i)=-1/sing*dcostau(j,2,3,i)
       !        write(iout,*) i,j,"else", dtauangle(j,2,3,i) 
       !        write(iout,*) i,j,"else", dtauangle(j,2,3,i) 
-             enddo
-            endif                                    
-            enddo
+           enddo
+          endif                                    
+          enddo
 
       !CC third case SC...Ca...Ca...SC
 #ifdef PARINTDER
 
 
       !CC third case SC...Ca...Ca...SC
 #ifdef PARINTDER
 
-            do i=itau_start,itau_end
+          do i=itau_start,itau_end
 #else
 #else
-            do i=3,nres
+          do i=3,nres
 #endif
       ! the conventional case
 #endif
       ! the conventional case
-            if ((itype(i-1,1).eq.ntyp1).or.(itype(i-1,1).eq.10).or. &
-            (itype(i-2,1).eq.ntyp1).or.(itype(i-2,1).eq.10)) cycle
-            sint=dsin(omicron(1,i))
-            sint1=dsin(omicron(2,i-1))
-            sing=dsin(tauangle(3,i))
-            cost=dcos(omicron(1,i))
-            cost1=dcos(omicron(2,i-1))
-            cosg=dcos(tauangle(3,i))
-            do j=1,3
-            dc_norm2(j,i-2+nres)=-dc_norm(j,i-2+nres)
+          if ((itype(i-1,1).eq.ntyp1).or.(itype(i-1,1).eq.10).or. &
+          (itype(i-2,1).eq.ntyp1).or.(itype(i-2,1).eq.10)) cycle
+          sint=dsin(omicron(1,i))
+          sint1=dsin(omicron(2,i-1))
+          sing=dsin(tauangle(3,i))
+          cost=dcos(omicron(1,i))
+          cost1=dcos(omicron(2,i-1))
+          cosg=dcos(tauangle(3,i))
+          do j=1,3
+          dc_norm2(j,i-2+nres)=-dc_norm(j,i-2+nres)
       !        dc_norm2(j,i-1+nres)=-dc_norm(j,i-1+nres)
       !        dc_norm2(j,i-1+nres)=-dc_norm(j,i-1+nres)
-            enddo
-            scalp=scalar(dc_norm2(1,i-2+nres),dc_norm(1,i-1+nres))
-            fac0=1.0d0/(sint1*sint)
-            fac1=cost*fac0
-            fac2=cost1*fac0
-            fac3=cosg*cost1/(sint1*sint1)
-            fac4=cosg*cost/(sint*sint)
+          enddo
+          scalp=scalar(dc_norm2(1,i-2+nres),dc_norm(1,i-1+nres))
+        if ((sint*sint1).eq.0.0d0) then
+          fac0=0.0d0
+          else
+          fac0=1.0d0/(sint1*sint)
+          endif
+          fac1=cost*fac0
+          fac2=cost1*fac0
+          if (sint1.ne.0.0d0) then
+          fac3=cosg*cost1/(sint1*sint1)
+          else
+          fac3=0.0d0
+          endif
+          if (sint.ne.0.0d0) then
+          fac4=cosg*cost/(sint*sint)
+          else
+          fac4=0.0d0
+          endif
       !    Obtaining the gamma derivatives from sine derivative                                
       !    Obtaining the gamma derivatives from sine derivative                                
-             if (tauangle(3,i).gt.-pi4.and.tauangle(3,i).le.pi4.or. &
-               tauangle(3,i).gt.pi34.and.tauangle(3,i).le.pi.or. &
-               tauangle(3,i).gt.-pi.and.tauangle(3,i).le.-pi34) then
-             call vecpr(dc_norm(1,i-1+nres),dc_norm(1,i-2),vp1)
-             call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-1+nres),vp2)
-             call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-2),vp3)
-            do j=1,3
-                ctgt=cost/sint
-                ctgt1=cost1/sint1
-                cosg_inv=1.0d0/cosg
-                dsintau(j,3,1,i)=-sing*ctgt1*domicron(j,2,2,i-1) &
-                  -(fac0*vp1(j)-sing*dc_norm(j,i-2+nres)) &
-                  *vbld_inv(i-2+nres)
-                dtauangle(j,3,1,i)=cosg_inv*dsintau(j,3,1,i)
-                dsintau(j,3,2,i)= &
-                  -sing*(ctgt1*domicron(j,2,1,i-1)+ctgt*domicron(j,1,1,i)) &
-                  -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1)
-                dtauangle(j,3,2,i)=cosg_inv*dsintau(j,3,2,i)
+           if (tauangle(3,i).gt.-pi4.and.tauangle(3,i).le.pi4.or. &
+             tauangle(3,i).gt.pi34.and.tauangle(3,i).le.pi.or. &
+             tauangle(3,i).gt.-pi.and.tauangle(3,i).le.-pi34) then
+           call vecpr(dc_norm(1,i-1+nres),dc_norm(1,i-2),vp1)
+           call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-1+nres),vp2)
+           call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-2),vp3)
+          do j=1,3
+            ctgt=cost/sint
+            ctgt1=cost1/sint1
+            cosg_inv=1.0d0/cosg
+            dsintau(j,3,1,i)=-sing*ctgt1*domicron(j,2,2,i-1) &
+              -(fac0*vp1(j)-sing*dc_norm(j,i-2+nres)) &
+              *vbld_inv(i-2+nres)
+            dtauangle(j,3,1,i)=cosg_inv*dsintau(j,3,1,i)
+            dsintau(j,3,2,i)= &
+              -sing*(ctgt1*domicron(j,2,1,i-1)+ctgt*domicron(j,1,1,i)) &
+              -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1)
+            dtauangle(j,3,2,i)=cosg_inv*dsintau(j,3,2,i)
       ! Bug fixed 3/24/05 (AL)
       ! Bug fixed 3/24/05 (AL)
-                dsintau(j,3,3,i)=-sing*ctgt*domicron(j,1,2,i) &
-                  +(fac0*vp3(j)-sing*dc_norm(j,i-1+nres)) &
-                  *vbld_inv(i-1+nres)
+            dsintau(j,3,3,i)=-sing*ctgt*domicron(j,1,2,i) &
+              +(fac0*vp3(j)-sing*dc_norm(j,i-1+nres)) &
+              *vbld_inv(i-1+nres)
       !     &        +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1)
       !     &        +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1)
-                dtauangle(j,3,3,i)=cosg_inv*dsintau(j,3,3,i)
-             enddo
+            dtauangle(j,3,3,i)=cosg_inv*dsintau(j,3,3,i)
+           enddo
       !   Obtaining the gamma derivatives from cosine derivative
       !   Obtaining the gamma derivatives from cosine derivative
-            else
-               do j=1,3
-               dcostau(j,3,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3* &
-               dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp* &
-               dc_norm2(j,i-2+nres))/vbld(i-2+nres)
-               dtauangle(j,3,1,i)=-1/sing*dcostau(j,3,1,i)
-               dcostau(j,3,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2* &
-               dcosomicron(j,1,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4* &
-               dcosomicron(j,1,1,i)
-               dtauangle(j,3,2,i)=-1/sing*dcostau(j,3,2,i)
-               dcostau(j,3,3,i)=fac2*dcosomicron(j,1,2,i)+fac4* &
-               dcosomicron(j,1,2,i)-fac0*(dc_norm2(j,i-2+nres)-scalp* &
-               dc_norm(j,i-1+nres))/vbld(i-1+nres)
-               dtauangle(j,3,3,i)=-1/sing*dcostau(j,3,3,i)
+          else
+             do j=1,3
+             dcostau(j,3,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3* &
+             dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp* &
+             dc_norm2(j,i-2+nres))/vbld(i-2+nres)
+             dtauangle(j,3,1,i)=-1/sing*dcostau(j,3,1,i)
+             dcostau(j,3,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2* &
+             dcosomicron(j,1,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4* &
+             dcosomicron(j,1,1,i)
+             dtauangle(j,3,2,i)=-1/sing*dcostau(j,3,2,i)
+             dcostau(j,3,3,i)=fac2*dcosomicron(j,1,2,i)+fac4* &
+             dcosomicron(j,1,2,i)-fac0*(dc_norm2(j,i-2+nres)-scalp* &
+             dc_norm(j,i-1+nres))/vbld(i-1+nres)
+             dtauangle(j,3,3,i)=-1/sing*dcostau(j,3,3,i)
       !          write(iout,*) "else",i 
       !          write(iout,*) "else",i 
-             enddo
-            endif                                                                                            
-            enddo
+           enddo
+          endif                                                                                            
+          enddo
 
 #ifdef CRYST_SC
       !   Derivatives of side-chain angles alpha and omega
 #if defined(MPI) && defined(PARINTDER)
 
 #ifdef CRYST_SC
       !   Derivatives of side-chain angles alpha and omega
 #if defined(MPI) && defined(PARINTDER)
-            do i=ibond_start,ibond_end
+          do i=ibond_start,ibond_end
 #else
 #else
-            do i=2,nres-1          
+          do i=2,nres-1          
 #endif
 #endif
-              if(itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then        
-                 fac5=1.0d0/dsqrt(2*(1+dcos(theta(i+1))))
-                 fac6=fac5/vbld(i)
-                 fac7=fac5*fac5
-                 fac8=fac5/vbld(i+1)     
-                 fac9=fac5/vbld(i+nres)                      
-                 scala1=scalar(dc_norm(1,i-1),dc_norm(1,i+nres))
-                 scala2=scalar(dc_norm(1,i),dc_norm(1,i+nres))
-                 cosa=dsqrt(0.5d0/(1.0d0+dcos(theta(i+1))))* &
-                 (scalar(dC_norm(1,i),dC_norm(1,i+nres)) &
-                 -scalar(dC_norm(1,i-1),dC_norm(1,i+nres)))
-                 sina=sqrt(1-cosa*cosa)
-                 sino=dsin(omeg(i))                                                                                                                                
+            if(itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then        
+             fac5=1.0d0/dsqrt(2*(1+dcos(theta(i+1))))
+             fac6=fac5/vbld(i)
+             fac7=fac5*fac5
+             fac8=fac5/vbld(i+1)     
+             fac9=fac5/vbld(i+nres)                      
+             scala1=scalar(dc_norm(1,i-1),dc_norm(1,i+nres))
+             scala2=scalar(dc_norm(1,i),dc_norm(1,i+nres))
+             cosa=dsqrt(0.5d0/(1.0d0+dcos(theta(i+1))))* &
+             (scalar(dC_norm(1,i),dC_norm(1,i+nres)) &
+             -scalar(dC_norm(1,i-1),dC_norm(1,i+nres)))
+             sina=sqrt(1-cosa*cosa)
+             sino=dsin(omeg(i))                                                                                                                                
       !             write (iout,*) "i",i," cosa",cosa," sina",sina," sino",sino
       !             write (iout,*) "i",i," cosa",cosa," sina",sina," sino",sino
-                 do j=1,3        
-                  dcosalpha(j,1,i)=fac6*(scala1*dc_norm(j,i-1)- &
-                  dc_norm(j,i+nres))-cosa*fac7*dcostheta(j,1,i+1)
-                  dalpha(j,1,i)=-1/sina*dcosalpha(j,1,i)
-                  dcosalpha(j,2,i)=fac8*(dc_norm(j,i+nres)- &
-                  scala2*dc_norm(j,i))-cosa*fac7*dcostheta(j,2,i+1)
-                  dalpha(j,2,i)=-1/sina*dcosalpha(j,2,i)
-                  dcosalpha(j,3,i)=(fac9*(dc_norm(j,i)- &
-                  dc_norm(j,i-1))-(cosa*dc_norm(j,i+nres))/ &
-                  vbld(i+nres))
-                  dalpha(j,3,i)=-1/sina*dcosalpha(j,3,i)
-                enddo
+             do j=1,3        
+              dcosalpha(j,1,i)=fac6*(scala1*dc_norm(j,i-1)- &
+              dc_norm(j,i+nres))-cosa*fac7*dcostheta(j,1,i+1)
+              dalpha(j,1,i)=-1/sina*dcosalpha(j,1,i)
+              dcosalpha(j,2,i)=fac8*(dc_norm(j,i+nres)- &
+              scala2*dc_norm(j,i))-cosa*fac7*dcostheta(j,2,i+1)
+              dalpha(j,2,i)=-1/sina*dcosalpha(j,2,i)
+              dcosalpha(j,3,i)=(fac9*(dc_norm(j,i)- &
+              dc_norm(j,i-1))-(cosa*dc_norm(j,i+nres))/ &
+              vbld(i+nres))
+              dalpha(j,3,i)=-1/sina*dcosalpha(j,3,i)
+            enddo
       ! obtaining the derivatives of omega from sines          
       ! obtaining the derivatives of omega from sines          
-                if(omeg(i).gt.-pi4.and.omeg(i).le.pi4.or. &
-                   omeg(i).gt.pi34.and.omeg(i).le.pi.or. &
-                   omeg(i).gt.-pi.and.omeg(i).le.-pi34) then
-                   fac15=dcos(theta(i+1))/(dsin(theta(i+1))* &
-                   dsin(theta(i+1)))
-                   fac16=dcos(alph(i))/(dsin(alph(i))*dsin(alph(i)))
-                   fac17=1.0d0/(dsin(theta(i+1))*dsin(alph(i)))                   
-                   call vecpr(dc_norm(1,i+nres),dc_norm(1,i),vo1)
-                   call vecpr(dc_norm(1,i+nres),dc_norm(1,i-1),vo2)
-                   call vecpr(dc_norm(1,i),dc_norm(1,i-1),vo3)
-                   coso_inv=1.0d0/dcos(omeg(i))                                       
-                   do j=1,3
-                   dsinomega(j,1,i)=sino*(fac15*dcostheta(j,1,i+1) &
-                   +fac16*dcosalpha(j,1,i))-fac17/vbld(i)*vo1(j)- &
-                   (sino*dc_norm(j,i-1))/vbld(i)
-                   domega(j,1,i)=coso_inv*dsinomega(j,1,i)
-                   dsinomega(j,2,i)=sino*(fac15*dcostheta(j,2,i+1) &
-                   +fac16*dcosalpha(j,2,i))+fac17/vbld(i+1)*vo2(j) &
-                   -sino*dc_norm(j,i)/vbld(i+1)
-                   domega(j,2,i)=coso_inv*dsinomega(j,2,i)                                               
-                   dsinomega(j,3,i)=sino*fac16*dcosalpha(j,3,i)- &
-                   fac17/vbld(i+nres)*vo3(j)-sino*dc_norm(j,i+nres)/ &
-                   vbld(i+nres)
-                   domega(j,3,i)=coso_inv*dsinomega(j,3,i)
-                  enddo                           
-               else
-      !   obtaining the derivatives of omega from cosines
-                 fac10=sqrt(0.5d0*(1-dcos(theta(i+1))))
-                 fac11=sqrt(0.5d0*(1+dcos(theta(i+1))))
-                 fac12=fac10*sina
-                 fac13=fac12*fac12
-                 fac14=sina*sina
-                 do j=1,3                                     
-                  dcosomega(j,1,i)=(-(0.25d0*cosa/fac11* &
-                  dcostheta(j,1,i+1)+fac11*dcosalpha(j,1,i))*fac12+ &
-                  (0.25d0/fac10*sina*dcostheta(j,1,i+1)+cosa/sina* &
-                  fac10*dcosalpha(j,1,i))*(scala2-fac11*cosa))/fac13
-                  domega(j,1,i)=-1/sino*dcosomega(j,1,i)
-                  dcosomega(j,2,i)=(((dc_norm(j,i+nres)-scala2* &
-                  dc_norm(j,i))/vbld(i+1)-0.25d0*cosa/fac11* &
-                  dcostheta(j,2,i+1)-fac11*dcosalpha(j,2,i))*fac12+ &
-                  (scala2-fac11*cosa)*(0.25d0*sina/fac10* &
-                  dcostheta(j,2,i+1)+fac10*cosa/sina*dcosalpha(j,2,i)))/fac13
-                  domega(j,2,i)=-1/sino*dcosomega(j,2,i)             
-                  dcosomega(j,3,i)=1/fac10*((1/vbld(i+nres)*(dc_norm(j,i)- &
-                  scala2*dc_norm(j,i+nres))-fac11*dcosalpha(j,3,i))*sina+ &
-                  (scala2-fac11*cosa)*(cosa/sina*dcosalpha(j,3,i)))/fac14
-                  domega(j,3,i)=-1/sino*dcosomega(j,3,i)                         
-                enddo           
-              endif
-             else
+            if(omeg(i).gt.-pi4.and.omeg(i).le.pi4.or. &
+               omeg(i).gt.pi34.and.omeg(i).le.pi.or. &
+               omeg(i).gt.-pi.and.omeg(i).le.-pi34) then
+               fac15=dcos(theta(i+1))/(dsin(theta(i+1))* &
+               dsin(theta(i+1)))
+               fac16=dcos(alph(i))/(dsin(alph(i))*dsin(alph(i)))
+               fac17=1.0d0/(dsin(theta(i+1))*dsin(alph(i)))                   
+               call vecpr(dc_norm(1,i+nres),dc_norm(1,i),vo1)
+               call vecpr(dc_norm(1,i+nres),dc_norm(1,i-1),vo2)
+               call vecpr(dc_norm(1,i),dc_norm(1,i-1),vo3)
+               coso_inv=1.0d0/dcos(omeg(i))                                       
                do j=1,3
                do j=1,3
-                 do k=1,3
-                   dalpha(k,j,i)=0.0d0
-                   domega(k,j,i)=0.0d0
-                 enddo
-               enddo
-             endif
-             enddo                                     
+               dsinomega(j,1,i)=sino*(fac15*dcostheta(j,1,i+1) &
+               +fac16*dcosalpha(j,1,i))-fac17/vbld(i)*vo1(j)- &
+               (sino*dc_norm(j,i-1))/vbld(i)
+               domega(j,1,i)=coso_inv*dsinomega(j,1,i)
+               dsinomega(j,2,i)=sino*(fac15*dcostheta(j,2,i+1) &
+               +fac16*dcosalpha(j,2,i))+fac17/vbld(i+1)*vo2(j) &
+               -sino*dc_norm(j,i)/vbld(i+1)
+               domega(j,2,i)=coso_inv*dsinomega(j,2,i)                                               
+               dsinomega(j,3,i)=sino*fac16*dcosalpha(j,3,i)- &
+               fac17/vbld(i+nres)*vo3(j)-sino*dc_norm(j,i+nres)/ &
+               vbld(i+nres)
+               domega(j,3,i)=coso_inv*dsinomega(j,3,i)
+              enddo                           
+             else
+      !   obtaining the derivatives of omega from cosines
+             fac10=sqrt(0.5d0*(1-dcos(theta(i+1))))
+             fac11=sqrt(0.5d0*(1+dcos(theta(i+1))))
+             fac12=fac10*sina
+             fac13=fac12*fac12
+             fac14=sina*sina
+             do j=1,3                                     
+              dcosomega(j,1,i)=(-(0.25d0*cosa/fac11* &
+              dcostheta(j,1,i+1)+fac11*dcosalpha(j,1,i))*fac12+ &
+              (0.25d0/fac10*sina*dcostheta(j,1,i+1)+cosa/sina* &
+              fac10*dcosalpha(j,1,i))*(scala2-fac11*cosa))/fac13
+              domega(j,1,i)=-1/sino*dcosomega(j,1,i)
+              dcosomega(j,2,i)=(((dc_norm(j,i+nres)-scala2* &
+              dc_norm(j,i))/vbld(i+1)-0.25d0*cosa/fac11* &
+              dcostheta(j,2,i+1)-fac11*dcosalpha(j,2,i))*fac12+ &
+              (scala2-fac11*cosa)*(0.25d0*sina/fac10* &
+              dcostheta(j,2,i+1)+fac10*cosa/sina*dcosalpha(j,2,i)))/fac13
+              domega(j,2,i)=-1/sino*dcosomega(j,2,i)             
+              dcosomega(j,3,i)=1/fac10*((1/vbld(i+nres)*(dc_norm(j,i)- &
+              scala2*dc_norm(j,i+nres))-fac11*dcosalpha(j,3,i))*sina+ &
+              (scala2-fac11*cosa)*(cosa/sina*dcosalpha(j,3,i)))/fac14
+              domega(j,3,i)=-1/sino*dcosomega(j,3,i)                         
+            enddo           
+            endif
+           else
+             do j=1,3
+             do k=1,3
+               dalpha(k,j,i)=0.0d0
+               domega(k,j,i)=0.0d0
+             enddo
+             enddo
+           endif
+           enddo                                     
 #endif
 #if defined(MPI) && defined(PARINTDER)
 #endif
 #if defined(MPI) && defined(PARINTDER)
-            if (nfgtasks.gt.1) then
+          if (nfgtasks.gt.1) then
 #ifdef DEBUG
       !d      write (iout,*) "Gather dtheta"
       !d      call flush(iout)
 #ifdef DEBUG
       !d      write (iout,*) "Gather dtheta"
       !d      call flush(iout)
-            write (iout,*) "dtheta before gather"
-            do i=1,nres
-            write (iout,'(i3,3(3f8.5,3x))') i,((dtheta(j,k,i),k=1,3),j=1,2)
-            enddo
+          write (iout,*) "dtheta before gather"
+          do i=1,nres
+          write (iout,'(i3,3(3f8.5,3x))') i,((dtheta(j,k,i),k=1,3),j=1,2)
+          enddo
 #endif
 #endif
-            call MPI_Gatherv(dtheta(1,1,ithet_start),ithet_count(fg_rank),&
-            MPI_THET,dtheta(1,1,1),ithet_count(0),ithet_displ(0),MPI_THET,&
-            king,FG_COMM,IERROR)
+          call MPI_Gatherv(dtheta(1,1,ithet_start),ithet_count(fg_rank),&
+          MPI_THET,dtheta(1,1,1),ithet_count(0),ithet_displ(0),MPI_THET,&
+          king,FG_COMM,IERROR)
 !#define DEBUG
 #ifdef DEBUG
       !d      write (iout,*) "Gather dphi"
       !d      call flush(iout)
 !#define DEBUG
 #ifdef DEBUG
       !d      write (iout,*) "Gather dphi"
       !d      call flush(iout)
-            write (iout,*) "dphi before gather"
-            do i=1,nres
-            write (iout,'(i3,3(3f8.5,3x))') i,((dphi(j,k,i),k=1,3),j=1,3)
-            enddo
+          write (iout,*) "dphi before gather"
+          do i=1,nres
+          write (iout,'(i3,3(3f8.5,3x))') i,((dphi(j,k,i),k=1,3),j=1,3)
+          enddo
 #endif
 !#undef DEBUG
 #endif
 !#undef DEBUG
-            call MPI_Gatherv(dphi(1,1,iphi1_start),iphi1_count(fg_rank),&
-            MPI_GAM,dphi(1,1,1),iphi1_count(0),iphi1_displ(0),MPI_GAM,&
-            king,FG_COMM,IERROR)
+          call MPI_Gatherv(dphi(1,1,iphi1_start),iphi1_count(fg_rank),&
+          MPI_GAM,dphi(1,1,1),iphi1_count(0),iphi1_displ(0),MPI_GAM,&
+          king,FG_COMM,IERROR)
       !d      write (iout,*) "Gather dalpha"
       !d      call flush(iout)
 #ifdef CRYST_SC
       !d      write (iout,*) "Gather dalpha"
       !d      call flush(iout)
 #ifdef CRYST_SC
-            call MPI_Gatherv(dalpha(1,1,ibond_start),ibond_count(fg_rank),&
-            MPI_GAM,dalpha(1,1,1),ibond_count(0),ibond_displ(0),MPI_GAM,&
-            king,FG_COMM,IERROR)
+          call MPI_Gatherv(dalpha(1,1,ibond_start),ibond_count(fg_rank),&
+          MPI_GAM,dalpha(1,1,1),ibond_count(0),ibond_displ(0),MPI_GAM,&
+          king,FG_COMM,IERROR)
       !d      write (iout,*) "Gather domega"
       !d      call flush(iout)
       !d      write (iout,*) "Gather domega"
       !d      call flush(iout)
-            call MPI_Gatherv(domega(1,1,ibond_start),ibond_count(fg_rank),&
-            MPI_GAM,domega(1,1,1),ibond_count(0),ibond_displ(0),MPI_GAM,&
-            king,FG_COMM,IERROR)
+          call MPI_Gatherv(domega(1,1,ibond_start),ibond_count(fg_rank),&
+          MPI_GAM,domega(1,1,1),ibond_count(0),ibond_displ(0),MPI_GAM,&
+          king,FG_COMM,IERROR)
 #endif
 #endif
-            endif
+          endif
 #endif
 !#define DEBUG
 #ifdef DEBUG
 #endif
 !#define DEBUG
 #ifdef DEBUG
-            write (iout,*) "dtheta after gather"
-            do i=1,nres
-            write (iout,'(i3,3(3f8.5,3x))') i,((dtheta(j,k,i),j=1,3),k=1,2)
-            enddo
-            write (iout,*) "dphi after gather"
-            do i=1,nres
-            write (iout,'(i3,3(3f8.5,3x))') i,((dphi(j,k,i),j=1,3),k=1,3)
-            enddo
-            write (iout,*) "dalpha after gather"
-            do i=1,nres
-            write (iout,'(i3,3(3f8.5,3x))') i,((dalpha(j,k,i),j=1,3),k=1,3)
-            enddo
-            write (iout,*) "domega after gather"
-            do i=1,nres
-            write (iout,'(i3,3(3f8.5,3x))') i,((domega(j,k,i),j=1,3),k=1,3)
-            enddo
+          write (iout,*) "dtheta after gather"
+          do i=1,nres
+          write (iout,'(i3,3(3f8.5,3x))') i,((dtheta(j,k,i),j=1,3),k=1,2)
+          enddo
+          write (iout,*) "dphi after gather"
+          do i=1,nres
+          write (iout,'(i3,3(3f8.5,3x))') i,((dphi(j,k,i),j=1,3),k=1,3)
+          enddo
+          write (iout,*) "dalpha after gather"
+          do i=1,nres
+          write (iout,'(i3,3(3f8.5,3x))') i,((dalpha(j,k,i),j=1,3),k=1,3)
+          enddo
+          write (iout,*) "domega after gather"
+          do i=1,nres
+          write (iout,'(i3,3(3f8.5,3x))') i,((domega(j,k,i),j=1,3),k=1,3)
+          enddo
 #endif
 !#undef DEBUG
 #endif
 !#undef DEBUG
-            return
-            end subroutine intcartderiv
+          return
+          end subroutine intcartderiv
       !-----------------------------------------------------------------------------
       !-----------------------------------------------------------------------------
-            subroutine checkintcartgrad
+          subroutine checkintcartgrad
       !      implicit real*8 (a-h,o-z)
       !      include 'DIMENSIONS'
 #ifdef MPI
       !      implicit real*8 (a-h,o-z)
       !      include 'DIMENSIONS'
 #ifdef MPI
-            include 'mpif.h'
+          include 'mpif.h'
 #endif
       !      include 'COMMON.CHAIN' 
       !      include 'COMMON.VAR'
 #endif
       !      include 'COMMON.CHAIN' 
       !      include 'COMMON.VAR'
@@ -17958,37 +17680,37 @@
       !      include 'COMMON.DERIV'
       !      include 'COMMON.IOUNITS'
       !      include 'COMMON.SETUP'
       !      include 'COMMON.DERIV'
       !      include 'COMMON.IOUNITS'
       !      include 'COMMON.SETUP'
-            real(kind=8),dimension(3,2,nres) :: dthetanum !(3,2,maxres)
-            real(kind=8),dimension(3,3,nres) :: dphinum,dalphanum,domeganum !(3,3,maxres)
-            real(kind=8),dimension(nres) :: theta_s,phi_s,alph_s,omeg_s !(maxres)
-            real(kind=8),dimension(3) :: dc_norm_s
-            real(kind=8) :: aincr=1.0d-5
-            integer :: i,j 
-            real(kind=8) :: dcji
-            do i=1,nres
-            phi_s(i)=phi(i)
-            theta_s(i)=theta(i)       
-            alph_s(i)=alph(i)
-            omeg_s(i)=omeg(i)
-            enddo
+          real(kind=8),dimension(3,2,nres) :: dthetanum !(3,2,maxres)
+          real(kind=8),dimension(3,3,nres) :: dphinum,dalphanum,domeganum !(3,3,maxres)
+          real(kind=8),dimension(nres) :: theta_s,phi_s,alph_s,omeg_s !(maxres)
+          real(kind=8),dimension(3) :: dc_norm_s
+          real(kind=8) :: aincr=1.0d-5
+          integer :: i,j 
+          real(kind=8) :: dcji
+          do i=1,nres
+          phi_s(i)=phi(i)
+          theta_s(i)=theta(i)       
+          alph_s(i)=alph(i)
+          omeg_s(i)=omeg(i)
+          enddo
       ! Check theta gradient
       ! Check theta gradient
-            write (iout,*) &
-             "Analytical (upper) and numerical (lower) gradient of theta"
-            write (iout,*) 
-            do i=3,nres
-            do j=1,3
-              dcji=dc(j,i-2)
-              dc(j,i-2)=dcji+aincr
-              call chainbuild_cart
-              call int_from_cart1(.false.)
-          dthetanum(j,1,i)=(theta(i)-theta_s(i))/aincr 
-          dc(j,i-2)=dcji
-          dcji=dc(j,i-1)
-          dc(j,i-1)=dc(j,i-1)+aincr
-          call chainbuild_cart        
-          dthetanum(j,2,i)=(theta(i)-theta_s(i))/aincr
-          dc(j,i-1)=dcji
-        enddo 
+          write (iout,*) &
+           "Analytical (upper) and numerical (lower) gradient of theta"
+          write (iout,*) 
+          do i=3,nres
+          do j=1,3
+            dcji=dc(j,i-2)
+            dc(j,i-2)=dcji+aincr
+            call chainbuild_cart
+            call int_from_cart1(.false.)
+        dthetanum(j,1,i)=(theta(i)-theta_s(i))/aincr 
+        dc(j,i-2)=dcji
+        dcji=dc(j,i-1)
+        dc(j,i-1)=dc(j,i-1)+aincr
+        call chainbuild_cart        
+        dthetanum(j,2,i)=(theta(i)-theta_s(i))/aincr
+        dc(j,i-1)=dcji
+      enddo 
 !el        write (iout,'(i5,3f10.5,5x,3f10.5)') i,(dtheta(j,1,i),j=1,3),&
 !el          (dtheta(j,2,i),j=1,3)
 !el        write (iout,'(5x,3f10.5,5x,3f10.5)') (dthetanum(j,1,i),j=1,3),&
 !el        write (iout,'(i5,3f10.5,5x,3f10.5)') i,(dtheta(j,1,i),j=1,3),&
 !el          (dtheta(j,2,i),j=1,3)
 !el        write (iout,'(5x,3f10.5,5x,3f10.5)') (dthetanum(j,1,i),j=1,3),&
@@ -18002,23 +17724,23 @@
       write (iout,*) &
        "Analytical (upper) and numerical (lower) gradient of gamma"
       do i=4,nres
       write (iout,*) &
        "Analytical (upper) and numerical (lower) gradient of gamma"
       do i=4,nres
-        do j=1,3
-          dcji=dc(j,i-3)
-          dc(j,i-3)=dcji+aincr
-          call chainbuild_cart
-          dphinum(j,1,i)=(phi(i)-phi_s(i))/aincr  
-              dc(j,i-3)=dcji
-          dcji=dc(j,i-2)
-          dc(j,i-2)=dcji+aincr
-          call chainbuild_cart
-          dphinum(j,2,i)=(phi(i)-phi_s(i))/aincr 
-          dc(j,i-2)=dcji
-          dcji=dc(j,i-1)
-          dc(j,i-1)=dc(j,i-1)+aincr
-          call chainbuild_cart
-          dphinum(j,3,i)=(phi(i)-phi_s(i))/aincr
-          dc(j,i-1)=dcji
-        enddo 
+      do j=1,3
+        dcji=dc(j,i-3)
+        dc(j,i-3)=dcji+aincr
+        call chainbuild_cart
+        dphinum(j,1,i)=(phi(i)-phi_s(i))/aincr  
+            dc(j,i-3)=dcji
+        dcji=dc(j,i-2)
+        dc(j,i-2)=dcji+aincr
+        call chainbuild_cart
+        dphinum(j,2,i)=(phi(i)-phi_s(i))/aincr 
+        dc(j,i-2)=dcji
+        dcji=dc(j,i-1)
+        dc(j,i-1)=dc(j,i-1)+aincr
+        call chainbuild_cart
+        dphinum(j,3,i)=(phi(i)-phi_s(i))/aincr
+        dc(j,i-1)=dcji
+      enddo 
 !el        write (iout,'(i5,3(3f10.5,5x))') i,(dphi(j,1,i),j=1,3),&
 !el          (dphi(j,2,i),j=1,3),(dphi(j,3,i),j=1,3)
 !el        write (iout,'(5x,3(3f10.5,5x))') (dphinum(j,1,i),j=1,3),&
 !el        write (iout,'(i5,3(3f10.5,5x))') i,(dphi(j,1,i),j=1,3),&
 !el          (dphi(j,2,i),j=1,3),(dphi(j,3,i),j=1,3)
 !el        write (iout,'(5x,3(3f10.5,5x))') (dphinum(j,1,i),j=1,3),&
@@ -18034,27 +17756,27 @@
        "Analytical (upper) and numerical (lower) gradient of alpha"
       do i=2,nres-1
        if(itype(i,1).ne.10) then
        "Analytical (upper) and numerical (lower) gradient of alpha"
       do i=2,nres-1
        if(itype(i,1).ne.10) then
-                 do j=1,3
-                  dcji=dc(j,i-1)
-                   dc(j,i-1)=dcji+aincr
-              call chainbuild_cart
-              dalphanum(j,1,i)=(alph(i)-alph_s(i)) &
-                 /aincr  
-                  dc(j,i-1)=dcji
-              dcji=dc(j,i)
-              dc(j,i)=dcji+aincr
-              call chainbuild_cart
-              dalphanum(j,2,i)=(alph(i)-alph_s(i)) &
-                 /aincr 
-              dc(j,i)=dcji
-              dcji=dc(j,i+nres)
-              dc(j,i+nres)=dc(j,i+nres)+aincr
-              call chainbuild_cart
-              dalphanum(j,3,i)=(alph(i)-alph_s(i)) &
-                 /aincr
-             dc(j,i+nres)=dcji
-            enddo
-          endif           
+             do j=1,3
+              dcji=dc(j,i-1)
+               dc(j,i-1)=dcji+aincr
+            call chainbuild_cart
+            dalphanum(j,1,i)=(alph(i)-alph_s(i)) &
+             /aincr  
+              dc(j,i-1)=dcji
+            dcji=dc(j,i)
+            dc(j,i)=dcji+aincr
+            call chainbuild_cart
+            dalphanum(j,2,i)=(alph(i)-alph_s(i)) &
+             /aincr 
+            dc(j,i)=dcji
+            dcji=dc(j,i+nres)
+            dc(j,i+nres)=dc(j,i+nres)+aincr
+            call chainbuild_cart
+            dalphanum(j,3,i)=(alph(i)-alph_s(i)) &
+             /aincr
+           dc(j,i+nres)=dcji
+          enddo
+        endif           
 !el        write (iout,'(i5,3(3f10.5,5x))') i,(dalpha(j,1,i),j=1,3),&
 !el          (dalpha(j,2,i),j=1,3),(dalpha(j,3,i),j=1,3)
 !el        write (iout,'(5x,3(3f10.5,5x))') (dalphanum(j,1,i),j=1,3),&
 !el        write (iout,'(i5,3(3f10.5,5x))') i,(dalpha(j,1,i),j=1,3),&
 !el          (dalpha(j,2,i),j=1,3),(dalpha(j,3,i),j=1,3)
 !el        write (iout,'(5x,3(3f10.5,5x))') (dalphanum(j,1,i),j=1,3),&
@@ -18070,27 +17792,27 @@
        "Analytical (upper) and numerical (lower) gradient of omega"
       do i=2,nres-1
        if(itype(i,1).ne.10) then
        "Analytical (upper) and numerical (lower) gradient of omega"
       do i=2,nres-1
        if(itype(i,1).ne.10) then
-                 do j=1,3
-                  dcji=dc(j,i-1)
-                   dc(j,i-1)=dcji+aincr
-              call chainbuild_cart
-              domeganum(j,1,i)=(omeg(i)-omeg_s(i)) &
-                 /aincr  
-                  dc(j,i-1)=dcji
-              dcji=dc(j,i)
-              dc(j,i)=dcji+aincr
-              call chainbuild_cart
-              domeganum(j,2,i)=(omeg(i)-omeg_s(i)) &
-                 /aincr 
-              dc(j,i)=dcji
-              dcji=dc(j,i+nres)
-              dc(j,i+nres)=dc(j,i+nres)+aincr
-              call chainbuild_cart
-              domeganum(j,3,i)=(omeg(i)-omeg_s(i)) &
-                 /aincr
-             dc(j,i+nres)=dcji
-            enddo
-          endif           
+             do j=1,3
+              dcji=dc(j,i-1)
+               dc(j,i-1)=dcji+aincr
+            call chainbuild_cart
+            domeganum(j,1,i)=(omeg(i)-omeg_s(i)) &
+             /aincr  
+              dc(j,i-1)=dcji
+            dcji=dc(j,i)
+            dc(j,i)=dcji+aincr
+            call chainbuild_cart
+            domeganum(j,2,i)=(omeg(i)-omeg_s(i)) &
+             /aincr 
+            dc(j,i)=dcji
+            dcji=dc(j,i+nres)
+            dc(j,i+nres)=dc(j,i+nres)+aincr
+            call chainbuild_cart
+            domeganum(j,3,i)=(omeg(i)-omeg_s(i)) &
+             /aincr
+           dc(j,i+nres)=dcji
+          enddo
+        endif           
 !el        write (iout,'(i5,3(3f10.5,5x))') i,(domega(j,1,i),j=1,3),&
 !el          (domega(j,2,i),j=1,3),(domega(j,3,i),j=1,3)
 !el        write (iout,'(5x,3(3f10.5,5x))') (domeganum(j,1,i),j=1,3),&
 !el        write (iout,'(i5,3(3f10.5,5x))') i,(domega(j,1,i),j=1,3),&
 !el          (domega(j,2,i),j=1,3),(domega(j,3,i),j=1,3)
 !el        write (iout,'(5x,3(3f10.5,5x))') (domeganum(j,1,i),j=1,3),&
@@ -18127,53 +17849,53 @@
       qq = 0.0d0
       nl=0 
        if(flag) then
       qq = 0.0d0
       nl=0 
        if(flag) then
-        do il=seg1+nsep,seg2
-          do jl=seg1,il-nsep
+      do il=seg1+nsep,seg2
+        do jl=seg1,il-nsep
+          nl=nl+1
+          d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2 + &
+                   (cref(2,jl,kkk)-cref(2,il,kkk))**2 + &
+                   (cref(3,jl,kkk)-cref(3,il,kkk))**2)
+          dij=dist(il,jl)
+          qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
+          if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then
             nl=nl+1
             nl=nl+1
-            d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2 + &
-                       (cref(2,jl,kkk)-cref(2,il,kkk))**2 + &
-                       (cref(3,jl,kkk)-cref(3,il,kkk))**2)
-            dij=dist(il,jl)
-            qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
-            if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then
-              nl=nl+1
-              d0ijCM=dsqrt( &
-                     (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
-                     (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
-                     (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
-              dijCM=dist(il+nres,jl+nres)
-              qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
-            endif
-            qq = qq+qqij+qqijCM
-          enddo
-        enddo       
-        qq = qq/nl
+            d0ijCM=dsqrt( &
+                 (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
+                 (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
+                 (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
+            dijCM=dist(il+nres,jl+nres)
+            qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
+          endif
+          qq = qq+qqij+qqijCM
+        enddo
+      enddo       
+      qq = qq/nl
       else
       do il=seg1,seg2
       else
       do il=seg1,seg2
-        if((seg3-il).lt.3) then
-             secseg=il+3
-        else
-             secseg=seg3
-        endif 
-          do jl=secseg,seg4
+      if((seg3-il).lt.3) then
+           secseg=il+3
+      else
+           secseg=seg3
+      endif 
+        do jl=secseg,seg4
+          nl=nl+1
+          d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
+                   (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
+                   (cref(3,jl,kkk)-cref(3,il,kkk))**2)
+          dij=dist(il,jl)
+          qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
+          if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then
             nl=nl+1
             nl=nl+1
-            d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
-                       (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
-                       (cref(3,jl,kkk)-cref(3,il,kkk))**2)
-            dij=dist(il,jl)
-            qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
-            if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then
-              nl=nl+1
-              d0ijCM=dsqrt( &
-                     (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
-                     (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
-                     (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
-              dijCM=dist(il+nres,jl+nres)
-              qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
-            endif
-            qq = qq+qqij+qqijCM
-          enddo
+            d0ijCM=dsqrt( &
+                 (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
+                 (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
+                 (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
+            dijCM=dist(il+nres,jl+nres)
+            qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
+          endif
+          qq = qq+qqij+qqijCM
         enddo
         enddo
+      enddo
       qq = qq/nl
       endif
       if (qqmax.le.qq) qqmax=qq
       qq = qq/nl
       endif
       if (qqmax.le.qq) qqmax=qq
@@ -18200,97 +17922,97 @@
 !el      sigm(x)=0.25d0*x           ! local function
       do kkk=1,nperm 
       do i=0,nres
 !el      sigm(x)=0.25d0*x           ! local function
       do kkk=1,nperm 
       do i=0,nres
-        do j=1,3
-          dqwol(j,i)=0.0d0
-          dxqwol(j,i)=0.0d0        
-        enddo
+      do j=1,3
+        dqwol(j,i)=0.0d0
+        dxqwol(j,i)=0.0d0        
+      enddo
       enddo
       nl=0 
        if(flag) then
       enddo
       nl=0 
        if(flag) then
-        do il=seg1+nsep,seg2
-          do jl=seg1,il-nsep
-            nl=nl+1
-            d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
-                       (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
-                       (cref(3,jl,kkk)-cref(3,il,kkk))**2)
-            dij=dist(il,jl)
-            sim = 1.0d0/sigm(d0ij)
-            sim = sim*sim
-            dd0 = dij-d0ij
-            fac = dd0*sim/dij*dexp(-0.5d0*dd0*dd0*sim)
-          do k=1,3
-              ddqij = (c(k,il)-c(k,jl))*fac
-              dqwol(k,il)=dqwol(k,il)+ddqij
-              dqwol(k,jl)=dqwol(k,jl)-ddqij
-            enddo
-                       
-            if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then
-              nl=nl+1
-              d0ijCM=dsqrt( &
-                     (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
-                     (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
-                     (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
-              dijCM=dist(il+nres,jl+nres)
-              sim = 1.0d0/sigm(d0ijCM)
-              sim = sim*sim
-              dd0=dijCM-d0ijCM
-              fac=dd0*sim/dijCM*dexp(-0.5d0*dd0*dd0*sim)
-              do k=1,3
-                ddqij = (c(k,il+nres)-c(k,jl+nres))*fac
-                dxqwol(k,il)=dxqwol(k,il)+ddqij
-                dxqwol(k,jl)=dxqwol(k,jl)-ddqij
-              enddo
-            endif           
+      do il=seg1+nsep,seg2
+        do jl=seg1,il-nsep
+          nl=nl+1
+          d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
+                   (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
+                   (cref(3,jl,kkk)-cref(3,il,kkk))**2)
+          dij=dist(il,jl)
+          sim = 1.0d0/sigm(d0ij)
+          sim = sim*sim
+          dd0 = dij-d0ij
+          fac = dd0*sim/dij*dexp(-0.5d0*dd0*dd0*sim)
+        do k=1,3
+            ddqij = (c(k,il)-c(k,jl))*fac
+            dqwol(k,il)=dqwol(k,il)+ddqij
+            dqwol(k,jl)=dqwol(k,jl)-ddqij
           enddo
           enddo
-        enddo       
-       else
-        do il=seg1,seg2
-        if((seg3-il).lt.3) then
-             secseg=il+3
-        else
-             secseg=seg3
-        endif 
-          do jl=secseg,seg4
+                   
+          if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then
             nl=nl+1
             nl=nl+1
-            d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
-                       (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
-                       (cref(3,jl,kkk)-cref(3,il,kkk))**2)
-            dij=dist(il,jl)
-            sim = 1.0d0/sigm(d0ij)
+            d0ijCM=dsqrt( &
+                 (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
+                 (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
+                 (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
+            dijCM=dist(il+nres,jl+nres)
+            sim = 1.0d0/sigm(d0ijCM)
             sim = sim*sim
             sim = sim*sim
-            dd0 = dij-d0ij
-            fac = dd0*sim/dij*dexp(-0.5d0*dd0*dd0*sim)
+            dd0=dijCM-d0ijCM
+            fac=dd0*sim/dijCM*dexp(-0.5d0*dd0*dd0*sim)
             do k=1,3
             do k=1,3
-              ddqij = (c(k,il)-c(k,jl))*fac
-              dqwol(k,il)=dqwol(k,il)+ddqij
-              dqwol(k,jl)=dqwol(k,jl)-ddqij
+            ddqij = (c(k,il+nres)-c(k,jl+nres))*fac
+            dxqwol(k,il)=dxqwol(k,il)+ddqij
+            dxqwol(k,jl)=dxqwol(k,jl)-ddqij
             enddo
             enddo
-            if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then
-              nl=nl+1
-              d0ijCM=dsqrt( &
-                     (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
-                     (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
-                     (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
-              dijCM=dist(il+nres,jl+nres)
-              sim = 1.0d0/sigm(d0ijCM)
-              sim=sim*sim
-              dd0 = dijCM-d0ijCM
-              fac = dd0*sim/dijCM*dexp(-0.5d0*dd0*dd0*sim)
-              do k=1,3
-               ddqij = (c(k,il+nres)-c(k,jl+nres))*fac             
-               dxqwol(k,il)=dxqwol(k,il)+ddqij
-               dxqwol(k,jl)=dxqwol(k,jl)-ddqij  
-              enddo
-            endif 
-          enddo
-        enddo                   
-      endif
-      enddo
+          endif           
+        enddo
+      enddo       
+       else
+      do il=seg1,seg2
+      if((seg3-il).lt.3) then
+           secseg=il+3
+      else
+           secseg=seg3
+      endif 
+        do jl=secseg,seg4
+          nl=nl+1
+          d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
+                   (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
+                   (cref(3,jl,kkk)-cref(3,il,kkk))**2)
+          dij=dist(il,jl)
+          sim = 1.0d0/sigm(d0ij)
+          sim = sim*sim
+          dd0 = dij-d0ij
+          fac = dd0*sim/dij*dexp(-0.5d0*dd0*dd0*sim)
+          do k=1,3
+            ddqij = (c(k,il)-c(k,jl))*fac
+            dqwol(k,il)=dqwol(k,il)+ddqij
+            dqwol(k,jl)=dqwol(k,jl)-ddqij
+          enddo
+          if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then
+            nl=nl+1
+            d0ijCM=dsqrt( &
+                 (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
+                 (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
+                 (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
+            dijCM=dist(il+nres,jl+nres)
+            sim = 1.0d0/sigm(d0ijCM)
+            sim=sim*sim
+            dd0 = dijCM-d0ijCM
+            fac = dd0*sim/dijCM*dexp(-0.5d0*dd0*dd0*sim)
+            do k=1,3
+             ddqij = (c(k,il+nres)-c(k,jl+nres))*fac             
+             dxqwol(k,il)=dxqwol(k,il)+ddqij
+             dxqwol(k,jl)=dxqwol(k,jl)-ddqij  
+            enddo
+          endif 
+        enddo
+      enddo                   
+      endif
+      enddo
        do i=0,nres
        do i=0,nres
-         do j=1,3
-           dqwol(j,i)=dqwol(j,i)/nl
-           dxqwol(j,i)=dxqwol(j,i)/nl
-         enddo
+       do j=1,3
+         dqwol(j,i)=dqwol(j,i)/nl
+         dxqwol(j,i)=dxqwol(j,i)/nl
+       enddo
        enddo
       return
       end subroutine qwolynes_prim
        enddo
       return
       end subroutine qwolynes_prim
@@ -18311,24 +18033,24 @@
       integer :: i,j
 
       do i=0,nres
       integer :: i,j
 
       do i=0,nres
-        do j=1,3
-          q1=qwolynes(seg1,seg2,flag,seg3,seg4)
-          cdummy(j,i)=c(j,i)
-          c(j,i)=c(j,i)+delta
-          q2=qwolynes(seg1,seg2,flag,seg3,seg4)
-          qwolan(j,i)=(q2-q1)/delta
-          c(j,i)=cdummy(j,i)
-        enddo
+      do j=1,3
+        q1=qwolynes(seg1,seg2,flag,seg3,seg4)
+        cdummy(j,i)=c(j,i)
+        c(j,i)=c(j,i)+delta
+        q2=qwolynes(seg1,seg2,flag,seg3,seg4)
+        qwolan(j,i)=(q2-q1)/delta
+        c(j,i)=cdummy(j,i)
+      enddo
       enddo
       do i=0,nres
       enddo
       do i=0,nres
-        do j=1,3
-          q1=qwolynes(seg1,seg2,flag,seg3,seg4)
-          cdummy(j,i+nres)=c(j,i+nres)
-          c(j,i+nres)=c(j,i+nres)+delta
-          q2=qwolynes(seg1,seg2,flag,seg3,seg4)
-          qwolxan(j,i)=(q2-q1)/delta
-          c(j,i+nres)=cdummy(j,i+nres)
-        enddo
+      do j=1,3
+        q1=qwolynes(seg1,seg2,flag,seg3,seg4)
+        cdummy(j,i+nres)=c(j,i+nres)
+        c(j,i+nres)=c(j,i+nres)+delta
+        q2=qwolynes(seg1,seg2,flag,seg3,seg4)
+        qwolxan(j,i)=(q2-q1)/delta
+        c(j,i+nres)=cdummy(j,i+nres)
+      enddo
       enddo  
 !      write(iout,*) "Numerical Q carteisan gradients backbone: "
 !      do i=0,nct
       enddo  
 !      write(iout,*) "Numerical Q carteisan gradients backbone: "
 !      do i=0,nct
@@ -18364,26 +18086,26 @@
 !      include 'COMMON.TIME1'
       real(kind=8) :: uzap1,uzap2,hm1,hm2,hmnum,ucdelan
       real(kind=8),dimension(3,0:nres) :: dUcartan,dUxcartan,cdummy,&
 !      include 'COMMON.TIME1'
       real(kind=8) :: uzap1,uzap2,hm1,hm2,hmnum,ucdelan
       real(kind=8),dimension(3,0:nres) :: dUcartan,dUxcartan,cdummy,&
-                   duconst,duxconst
+               duconst,duxconst
       integer :: kstart,kend,lstart,lend,idummy
       real(kind=8) :: delta=1.0d-7
       integer :: i,j,k,ii
       do i=0,nres
       integer :: kstart,kend,lstart,lend,idummy
       real(kind=8) :: delta=1.0d-7
       integer :: i,j,k,ii
       do i=0,nres
-         do j=1,3
-            duconst(j,i)=0.0d0
-            dudconst(j,i)=0.0d0
-            duxconst(j,i)=0.0d0
-            dudxconst(j,i)=0.0d0
-         enddo
+       do j=1,3
+          duconst(j,i)=0.0d0
+          dudconst(j,i)=0.0d0
+          duxconst(j,i)=0.0d0
+          dudxconst(j,i)=0.0d0
+       enddo
       enddo
       Uconst=0.0d0
       do i=1,nfrag
       enddo
       Uconst=0.0d0
       do i=1,nfrag
-         qfrag(i)=qwolynes(ifrag(1,i,iset),ifrag(2,i,iset),.true.,&
-           idummy,idummy)
-         Uconst=Uconst+wfrag(i,iset)*harmonic(qfrag(i),qinfrag(i,iset))
+       qfrag(i)=qwolynes(ifrag(1,i,iset),ifrag(2,i,iset),.true.,&
+         idummy,idummy)
+       Uconst=Uconst+wfrag(i,iset)*harmonic(qfrag(i),qinfrag(i,iset))
 ! Calculating the derivatives of Constraint energy with respect to Q
 ! Calculating the derivatives of Constraint energy with respect to Q
-         Ucdfrag=wfrag(i,iset)*harmonicprim(qfrag(i),&
-           qinfrag(i,iset))
+       Ucdfrag=wfrag(i,iset)*harmonicprim(qfrag(i),&
+         qinfrag(i,iset))
 !         hm1=harmonic(qfrag(i,iset),qinfrag(i,iset))
 !             hm2=harmonic(qfrag(i,iset)+delta,qinfrag(i,iset))
 !         hmnum=(hm2-hm1)/delta              
 !         hm1=harmonic(qfrag(i,iset),qinfrag(i,iset))
 !             hm2=harmonic(qfrag(i,iset)+delta,qinfrag(i,iset))
 !         hmnum=(hm2-hm1)/delta              
@@ -18391,8 +18113,8 @@
 !     &   qinfrag(i,iset))
 !         write(iout,*) "harmonicnum frag", hmnum               
 ! Calculating the derivatives of Q with respect to cartesian coordinates
 !     &   qinfrag(i,iset))
 !         write(iout,*) "harmonicnum frag", hmnum               
 ! Calculating the derivatives of Q with respect to cartesian coordinates
-         call qwolynes_prim(ifrag(1,i,iset),ifrag(2,i,iset),.true.,&
-          idummy,idummy)
+       call qwolynes_prim(ifrag(1,i,iset),ifrag(2,i,iset),.true.,&
+        idummy,idummy)
 !         write(iout,*) "dqwol "
 !         do ii=1,nres
 !          write(iout,'(i5,3e15.5)') ii,(dqwol(j,ii),j=1,3)
 !         write(iout,*) "dqwol "
 !         do ii=1,nres
 !          write(iout,'(i5,3e15.5)') ii,(dqwol(j,ii),j=1,3)
@@ -18405,22 +18127,22 @@
 !        call qwol_num(ifrag(1,i,iset),ifrag(2,i,iset),.true.
 !     &  ,idummy,idummy)
 !  The gradients of Uconst in Cs
 !        call qwol_num(ifrag(1,i,iset),ifrag(2,i,iset),.true.
 !     &  ,idummy,idummy)
 !  The gradients of Uconst in Cs
-         do ii=0,nres
-            do j=1,3
-               duconst(j,ii)=dUconst(j,ii)+ucdfrag*dqwol(j,ii)
-               dUxconst(j,ii)=dUxconst(j,ii)+ucdfrag*dxqwol(j,ii)
-            enddo
-         enddo
+       do ii=0,nres
+          do j=1,3
+             duconst(j,ii)=dUconst(j,ii)+ucdfrag*dqwol(j,ii)
+             dUxconst(j,ii)=dUxconst(j,ii)+ucdfrag*dxqwol(j,ii)
+          enddo
+       enddo
       enddo      
       do i=1,npair
       enddo      
       do i=1,npair
-         kstart=ifrag(1,ipair(1,i,iset),iset)
-         kend=ifrag(2,ipair(1,i,iset),iset)
-         lstart=ifrag(1,ipair(2,i,iset),iset)
-         lend=ifrag(2,ipair(2,i,iset),iset)
-         qpair(i)=qwolynes(kstart,kend,.false.,lstart,lend)
-         Uconst=Uconst+wpair(i,iset)*harmonic(qpair(i),qinpair(i,iset))
+       kstart=ifrag(1,ipair(1,i,iset),iset)
+       kend=ifrag(2,ipair(1,i,iset),iset)
+       lstart=ifrag(1,ipair(2,i,iset),iset)
+       lend=ifrag(2,ipair(2,i,iset),iset)
+       qpair(i)=qwolynes(kstart,kend,.false.,lstart,lend)
+       Uconst=Uconst+wpair(i,iset)*harmonic(qpair(i),qinpair(i,iset))
 !  Calculating dU/dQ
 !  Calculating dU/dQ
-         Ucdpair=wpair(i,iset)*harmonicprim(qpair(i),qinpair(i,iset))
+       Ucdpair=wpair(i,iset)*harmonicprim(qpair(i),qinpair(i,iset))
 !         hm1=harmonic(qpair(i),qinpair(i,iset))
 !             hm2=harmonic(qpair(i)+delta,qinpair(i,iset))
 !         hmnum=(hm2-hm1)/delta              
 !         hm1=harmonic(qpair(i),qinpair(i,iset))
 !             hm2=harmonic(qpair(i)+delta,qinpair(i,iset))
 !         hmnum=(hm2-hm1)/delta              
@@ -18428,8 +18150,8 @@
 !     &   qinpair(i,iset))
 !         write(iout,*) "harmonicnum pair ", hmnum       
 ! Calculating dQ/dXi
 !     &   qinpair(i,iset))
 !         write(iout,*) "harmonicnum pair ", hmnum       
 ! Calculating dQ/dXi
-         call qwolynes_prim(kstart,kend,.false.,&
-          lstart,lend)
+       call qwolynes_prim(kstart,kend,.false.,&
+        lstart,lend)
 !         write(iout,*) "dqwol "
 !         do ii=1,nres
 !          write(iout,'(i5,3e15.5)') ii,(dqwol(j,ii),j=1,3)
 !         write(iout,*) "dqwol "
 !         do ii=1,nres
 !          write(iout,'(i5,3e15.5)') ii,(dqwol(j,ii),j=1,3)
@@ -18442,27 +18164,27 @@
 !        call qwol_num(kstart,kend,.false.
 !     &  ,lstart,lend)
 ! The gradients of Uconst in Cs
 !        call qwol_num(kstart,kend,.false.
 !     &  ,lstart,lend)
 ! The gradients of Uconst in Cs
-         do ii=0,nres
-            do j=1,3
-               duconst(j,ii)=dUconst(j,ii)+ucdpair*dqwol(j,ii)
-               dUxconst(j,ii)=dUxconst(j,ii)+ucdpair*dxqwol(j,ii)
-            enddo
-         enddo
+       do ii=0,nres
+          do j=1,3
+             duconst(j,ii)=dUconst(j,ii)+ucdpair*dqwol(j,ii)
+             dUxconst(j,ii)=dUxconst(j,ii)+ucdpair*dxqwol(j,ii)
+          enddo
+       enddo
       enddo
 !      write(iout,*) "Uconst inside subroutine ", Uconst
 ! Transforming the gradients from Cs to dCs for the backbone
       do i=0,nres
       enddo
 !      write(iout,*) "Uconst inside subroutine ", Uconst
 ! Transforming the gradients from Cs to dCs for the backbone
       do i=0,nres
-         do j=i+1,nres
-           do k=1,3
-             dudconst(k,i)=dudconst(k,i)+duconst(k,j)+duxconst(k,j)
-           enddo
+       do j=i+1,nres
+         do k=1,3
+           dudconst(k,i)=dudconst(k,i)+duconst(k,j)+duxconst(k,j)
          enddo
          enddo
+       enddo
       enddo
 !  Transforming the gradients from Cs to dCs for the side chains      
       do i=1,nres
       enddo
 !  Transforming the gradients from Cs to dCs for the side chains      
       do i=1,nres
-         do j=1,3
-           dudxconst(j,i)=duxconst(j,i)
-         enddo
+       do j=1,3
+         dudxconst(j,i)=duxconst(j,i)
+       enddo
       enddo                       
 !      write(iout,*) "dU/ddc backbone "
 !       do ii=0,nres
       enddo                       
 !      write(iout,*) "dU/ddc backbone "
 !       do ii=0,nres
@@ -18507,95 +18229,95 @@
 !     real(kind=8) :: 
 !     For the backbone
       do i=0,nres-1
 !     real(kind=8) :: 
 !     For the backbone
       do i=0,nres-1
-         do j=1,3
-            dUcartan(j,i)=0.0d0
-            cdummy(j,i)=dc(j,i)
-            dc(j,i)=dc(j,i)+delta
-            call chainbuild_cart
-          uzap2=0.0d0
-            do ii=1,nfrag
-             qfrag(ii)=qwolynes(ifrag(1,ii,iset),ifrag(2,ii,iset),.true.,&
-                idummy,idummy)
-               uzap2=uzap2+wfrag(ii,iset)*harmonic(qfrag(ii),&
-                qinfrag(ii,iset))
-            enddo
-            do ii=1,npair
-               kstart=ifrag(1,ipair(1,ii,iset),iset)
-               kend=ifrag(2,ipair(1,ii,iset),iset)
-               lstart=ifrag(1,ipair(2,ii,iset),iset)
-               lend=ifrag(2,ipair(2,ii,iset),iset)
-               qpair(ii)=qwolynes(kstart,kend,.false.,lstart,lend)
-               uzap2=uzap2+wpair(ii,iset)*harmonic(qpair(ii),&
-                 qinpair(ii,iset))
-            enddo
-            dc(j,i)=cdummy(j,i)
-            call chainbuild_cart
-            uzap1=0.0d0
-             do ii=1,nfrag
-             qfrag(ii)=qwolynes(ifrag(1,ii,iset),ifrag(2,ii,iset),.true.,&
-                idummy,idummy)
-               uzap1=uzap1+wfrag(ii,iset)*harmonic(qfrag(ii),&
-                qinfrag(ii,iset))
-            enddo
-            do ii=1,npair
-               kstart=ifrag(1,ipair(1,ii,iset),iset)
-               kend=ifrag(2,ipair(1,ii,iset),iset)
-               lstart=ifrag(1,ipair(2,ii,iset),iset)
-               lend=ifrag(2,ipair(2,ii,iset),iset)
-               qpair(ii)=qwolynes(kstart,kend,.false.,lstart,lend)
-               uzap1=uzap1+wpair(ii,iset)*harmonic(qpair(ii),&
-                qinpair(ii,iset))
-            enddo
-            ducartan(j,i)=(uzap2-uzap1)/(delta)          
-         enddo
+       do j=1,3
+          dUcartan(j,i)=0.0d0
+          cdummy(j,i)=dc(j,i)
+          dc(j,i)=dc(j,i)+delta
+          call chainbuild_cart
+        uzap2=0.0d0
+          do ii=1,nfrag
+           qfrag(ii)=qwolynes(ifrag(1,ii,iset),ifrag(2,ii,iset),.true.,&
+            idummy,idummy)
+             uzap2=uzap2+wfrag(ii,iset)*harmonic(qfrag(ii),&
+            qinfrag(ii,iset))
+          enddo
+          do ii=1,npair
+             kstart=ifrag(1,ipair(1,ii,iset),iset)
+             kend=ifrag(2,ipair(1,ii,iset),iset)
+             lstart=ifrag(1,ipair(2,ii,iset),iset)
+             lend=ifrag(2,ipair(2,ii,iset),iset)
+             qpair(ii)=qwolynes(kstart,kend,.false.,lstart,lend)
+             uzap2=uzap2+wpair(ii,iset)*harmonic(qpair(ii),&
+             qinpair(ii,iset))
+          enddo
+          dc(j,i)=cdummy(j,i)
+          call chainbuild_cart
+          uzap1=0.0d0
+           do ii=1,nfrag
+           qfrag(ii)=qwolynes(ifrag(1,ii,iset),ifrag(2,ii,iset),.true.,&
+            idummy,idummy)
+             uzap1=uzap1+wfrag(ii,iset)*harmonic(qfrag(ii),&
+            qinfrag(ii,iset))
+          enddo
+          do ii=1,npair
+             kstart=ifrag(1,ipair(1,ii,iset),iset)
+             kend=ifrag(2,ipair(1,ii,iset),iset)
+             lstart=ifrag(1,ipair(2,ii,iset),iset)
+             lend=ifrag(2,ipair(2,ii,iset),iset)
+             qpair(ii)=qwolynes(kstart,kend,.false.,lstart,lend)
+             uzap1=uzap1+wpair(ii,iset)*harmonic(qpair(ii),&
+            qinpair(ii,iset))
+          enddo
+          ducartan(j,i)=(uzap2-uzap1)/(delta)          
+       enddo
       enddo
 ! Calculating numerical gradients for dU/ddx
       do i=0,nres-1
       enddo
 ! Calculating numerical gradients for dU/ddx
       do i=0,nres-1
-         duxcartan(j,i)=0.0d0
-         do j=1,3
-            cdummy(j,i)=dc(j,i+nres)
-            dc(j,i+nres)=dc(j,i+nres)+delta
-            call chainbuild_cart
-          uzap2=0.0d0
-            do ii=1,nfrag
-             qfrag(ii)=qwolynes(ifrag(1,ii,iset),ifrag(2,ii,iset),.true.,&
-                idummy,idummy)
-               uzap2=uzap2+wfrag(ii,iset)*harmonic(qfrag(ii),&
-                qinfrag(ii,iset))
-            enddo
-            do ii=1,npair
-               kstart=ifrag(1,ipair(1,ii,iset),iset)
-               kend=ifrag(2,ipair(1,ii,iset),iset)
-               lstart=ifrag(1,ipair(2,ii,iset),iset)
-               lend=ifrag(2,ipair(2,ii,iset),iset)
-               qpair(ii)=qwolynes(kstart,kend,.false.,lstart,lend)
-               uzap2=uzap2+wpair(ii,iset)*harmonic(qpair(ii),&
-                qinpair(ii,iset))
-            enddo
-            dc(j,i+nres)=cdummy(j,i)
-            call chainbuild_cart
-            uzap1=0.0d0
-             do ii=1,nfrag
-               qfrag(ii)=qwolynes(ifrag(1,ii,iset),&
-                ifrag(2,ii,iset),.true.,idummy,idummy)
-               uzap1=uzap1+wfrag(ii,iset)*harmonic(qfrag(ii),&
-                qinfrag(ii,iset))
-            enddo
-            do ii=1,npair
-               kstart=ifrag(1,ipair(1,ii,iset),iset)
-               kend=ifrag(2,ipair(1,ii,iset),iset)
-               lstart=ifrag(1,ipair(2,ii,iset),iset)
-               lend=ifrag(2,ipair(2,ii,iset),iset)
-               qpair(ii)=qwolynes(kstart,kend,.false.,lstart,lend)
-               uzap1=uzap1+wpair(ii,iset)*harmonic(qpair(ii),&
-                qinpair(ii,iset))
-            enddo
-            duxcartan(j,i)=(uzap2-uzap1)/(delta)          
-         enddo
+       duxcartan(j,i)=0.0d0
+       do j=1,3
+          cdummy(j,i)=dc(j,i+nres)
+          dc(j,i+nres)=dc(j,i+nres)+delta
+          call chainbuild_cart
+        uzap2=0.0d0
+          do ii=1,nfrag
+           qfrag(ii)=qwolynes(ifrag(1,ii,iset),ifrag(2,ii,iset),.true.,&
+            idummy,idummy)
+             uzap2=uzap2+wfrag(ii,iset)*harmonic(qfrag(ii),&
+            qinfrag(ii,iset))
+          enddo
+          do ii=1,npair
+             kstart=ifrag(1,ipair(1,ii,iset),iset)
+             kend=ifrag(2,ipair(1,ii,iset),iset)
+             lstart=ifrag(1,ipair(2,ii,iset),iset)
+             lend=ifrag(2,ipair(2,ii,iset),iset)
+             qpair(ii)=qwolynes(kstart,kend,.false.,lstart,lend)
+             uzap2=uzap2+wpair(ii,iset)*harmonic(qpair(ii),&
+            qinpair(ii,iset))
+          enddo
+          dc(j,i+nres)=cdummy(j,i)
+          call chainbuild_cart
+          uzap1=0.0d0
+           do ii=1,nfrag
+             qfrag(ii)=qwolynes(ifrag(1,ii,iset),&
+            ifrag(2,ii,iset),.true.,idummy,idummy)
+             uzap1=uzap1+wfrag(ii,iset)*harmonic(qfrag(ii),&
+            qinfrag(ii,iset))
+          enddo
+          do ii=1,npair
+             kstart=ifrag(1,ipair(1,ii,iset),iset)
+             kend=ifrag(2,ipair(1,ii,iset),iset)
+             lstart=ifrag(1,ipair(2,ii,iset),iset)
+             lend=ifrag(2,ipair(2,ii,iset),iset)
+             qpair(ii)=qwolynes(kstart,kend,.false.,lstart,lend)
+             uzap1=uzap1+wpair(ii,iset)*harmonic(qpair(ii),&
+            qinpair(ii,iset))
+          enddo
+          duxcartan(j,i)=(uzap2-uzap1)/(delta)          
+       enddo
       enddo    
       write(iout,*) "Numerical dUconst/ddc backbone "
       do ii=0,nres
       enddo    
       write(iout,*) "Numerical dUconst/ddc backbone "
       do ii=0,nres
-        write(iout,'(i5,3e15.5)') ii,(dUcartan(j,ii),j=1,3)
+      write(iout,'(i5,3e15.5)') ii,(dUcartan(j,ii),j=1,3)
       enddo
 !      write(iout,*) "Numerical dUconst/ddx side-chain "
 !      do ii=1,nres
       enddo
 !      write(iout,*) "Numerical dUconst/ddx side-chain "
 !      do ii=1,nres
@@ -18644,10 +18366,10 @@
       pmax=1
 
       do k=1,3
       pmax=1
 
       do k=1,3
-        c(k,i)=0.0D0
-        c(k,j)=0.0D0
-        c(k,nres+i)=0.0D0
-        c(k,nres+j)=0.0D0
+      c(k,i)=0.0D0
+      c(k,j)=0.0D0
+      c(k,nres+i)=0.0D0
+      c(k,nres+j)=0.0D0
       enddo
 
       do l=1,lmax
       enddo
 
       do l=1,lmax
@@ -18660,27 +18382,27 @@
 !        pj=ran_number(0.0D0,pi/6.0D0)
 !        pj=0.0D0
 
 !        pj=ran_number(0.0D0,pi/6.0D0)
 !        pj=0.0D0
 
-        do p=1,pmax
+      do p=1,pmax
 !t           rij=ran_number(rmin,rmax)
 
 !t           rij=ran_number(rmin,rmax)
 
-           c(1,j)=d*sin(pj)*cos(tj)
-           c(2,j)=d*sin(pj)*sin(tj)
-           c(3,j)=d*cos(pj)
+         c(1,j)=d*sin(pj)*cos(tj)
+         c(2,j)=d*sin(pj)*sin(tj)
+         c(3,j)=d*cos(pj)
 
 
-           c(3,nres+i)=-rij
+         c(3,nres+i)=-rij
 
 
-           c(1,i)=d*sin(wi)
-           c(3,i)=-rij-d*cos(wi)
+         c(1,i)=d*sin(wi)
+         c(3,i)=-rij-d*cos(wi)
 
 
-           do k=1,3
-              dc(k,nres+i)=c(k,nres+i)-c(k,i)
-              dc_norm(k,nres+i)=dc(k,nres+i)/d
-              dc(k,nres+j)=c(k,nres+j)-c(k,j)
-              dc_norm(k,nres+j)=dc(k,nres+j)/d
-           enddo
+         do k=1,3
+            dc(k,nres+i)=c(k,nres+i)-c(k,i)
+            dc_norm(k,nres+i)=dc(k,nres+i)/d
+            dc(k,nres+j)=c(k,nres+j)-c(k,j)
+            dc_norm(k,nres+j)=dc(k,nres+j)/d
+         enddo
 
 
-           call dyn_ssbond_ene(i,j,eij)
-        enddo
+         call dyn_ssbond_ene(i,j,eij)
+      enddo
       enddo
       call exit(1)
       return
       enddo
       call exit(1)
       return
@@ -18810,8 +18532,8 @@
       ssA=akcm
       ssB=akct*deltat12
       ssC=ss_depth &
       ssA=akcm
       ssB=akct*deltat12
       ssC=ss_depth &
-           +akth*(deltat1*deltat1+deltat2*deltat2) &
-           +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi
+         +akth*(deltat1*deltat1+deltat2*deltat2) &
+         +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi
       ssxm=ssXs-0.5D0*ssB/ssA
 
 !-------TESTING CODE
       ssxm=ssXs-0.5D0*ssB/ssA
 
 !-------TESTING CODE
@@ -18833,119 +18555,119 @@
 !-------TESTING CODE
 !     Stop and plot energy and derivative as a function of distance
       if (checkstop) then
 !-------TESTING CODE
 !     Stop and plot energy and derivative as a function of distance
       if (checkstop) then
-        ssm=ssC-0.25D0*ssB*ssB/ssA
-        ljm=-0.25D0*ljB*bb_aq(itypi,itypj)/aa_aq(itypi,itypj)
-        if (ssm.lt.ljm .and. &
-             dabs(rij-0.5d0*(ssxm+ljxm)).lt.0.35d0*(ljxm-ssxm)) then
-          nicheck=1000
-          njcheck=1
-          deps=0.5d-7
-        else
-          checkstop=.false.
-        endif
+      ssm=ssC-0.25D0*ssB*ssB/ssA
+      ljm=-0.25D0*ljB*bb_aq(itypi,itypj)/aa_aq(itypi,itypj)
+      if (ssm.lt.ljm .and. &
+           dabs(rij-0.5d0*(ssxm+ljxm)).lt.0.35d0*(ljxm-ssxm)) then
+        nicheck=1000
+        njcheck=1
+        deps=0.5d-7
+      else
+        checkstop=.false.
+      endif
       endif
       if (.not.checkstop) then
       endif
       if (.not.checkstop) then
-        nicheck=0
-        njcheck=-1
+      nicheck=0
+      njcheck=-1
       endif
 
       do icheck=0,nicheck
       do jcheck=-1,njcheck
       if (checkstop) rij=(ssxm-1.0d0)+ &
       endif
 
       do icheck=0,nicheck
       do jcheck=-1,njcheck
       if (checkstop) rij=(ssxm-1.0d0)+ &
-             ((ljxm-ssxm+2.0d0)*icheck)/nicheck+jcheck*deps
+           ((ljxm-ssxm+2.0d0)*icheck)/nicheck+jcheck*deps
 !-------END TESTING CODE
 
       if (rij.gt.ljxm) then
 !-------END TESTING CODE
 
       if (rij.gt.ljxm) then
-        havebond=.false.
-        ljd=rij-ljXs
-        fac=(1.0D0/ljd)**expon
-        e1=fac*fac*aa_aq(itypi,itypj)
-        e2=fac*bb_aq(itypi,itypj)
-        eij=eps1*eps2rt*eps3rt*(e1+e2)
-        eps2der=eij*eps3rt
-        eps3der=eij*eps2rt
-        eij=eij*eps2rt*eps3rt
-
-        sigder=-sig/sigsq
-        e1=e1*eps1*eps2rt**2*eps3rt**2
-        ed=-expon*(e1+eij)/ljd
-        sigder=ed*sigder
-        eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1
-        eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2
-        eom12=eij*eps1_om12+eps2der*eps2rt_om12 &
-             -2.0D0*alf12*eps3der+sigder*sigsq_om12
+      havebond=.false.
+      ljd=rij-ljXs
+      fac=(1.0D0/ljd)**expon
+      e1=fac*fac*aa_aq(itypi,itypj)
+      e2=fac*bb_aq(itypi,itypj)
+      eij=eps1*eps2rt*eps3rt*(e1+e2)
+      eps2der=eij*eps3rt
+      eps3der=eij*eps2rt
+      eij=eij*eps2rt*eps3rt
+
+      sigder=-sig/sigsq
+      e1=e1*eps1*eps2rt**2*eps3rt**2
+      ed=-expon*(e1+eij)/ljd
+      sigder=ed*sigder
+      eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1
+      eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2
+      eom12=eij*eps1_om12+eps2der*eps2rt_om12 &
+           -2.0D0*alf12*eps3der+sigder*sigsq_om12
       else if (rij.lt.ssxm) then
       else if (rij.lt.ssxm) then
-        havebond=.true.
-        ssd=rij-ssXs
-        eij=ssA*ssd*ssd+ssB*ssd+ssC
-
-        ed=2*akcm*ssd+akct*deltat12
-        pom1=akct*ssd
-        pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi
-        eom1=-2*akth*deltat1-pom1-om2*pom2
-        eom2= 2*akth*deltat2+pom1-om1*pom2
-        eom12=pom2
+      havebond=.true.
+      ssd=rij-ssXs
+      eij=ssA*ssd*ssd+ssB*ssd+ssC
+
+      ed=2*akcm*ssd+akct*deltat12
+      pom1=akct*ssd
+      pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi
+      eom1=-2*akth*deltat1-pom1-om2*pom2
+      eom2= 2*akth*deltat2+pom1-om1*pom2
+      eom12=pom2
       else
       else
-        omega=v1ss+2.0d0*v2ss*cosphi+3.0d0*v3ss*cosphi*cosphi
+      omega=v1ss+2.0d0*v2ss*cosphi+3.0d0*v3ss*cosphi*cosphi
 
 
-        d_ssxm(1)=0.5D0*akct/ssA
-        d_ssxm(2)=-d_ssxm(1)
-        d_ssxm(3)=0.0D0
+      d_ssxm(1)=0.5D0*akct/ssA
+      d_ssxm(2)=-d_ssxm(1)
+      d_ssxm(3)=0.0D0
 
 
-        d_ljxm(1)=sig0ij/sqrt(sigsq**3)
-        d_ljxm(2)=d_ljxm(1)*sigsq_om2
-        d_ljxm(3)=d_ljxm(1)*sigsq_om12
-        d_ljxm(1)=d_ljxm(1)*sigsq_om1
+      d_ljxm(1)=sig0ij/sqrt(sigsq**3)
+      d_ljxm(2)=d_ljxm(1)*sigsq_om2
+      d_ljxm(3)=d_ljxm(1)*sigsq_om12
+      d_ljxm(1)=d_ljxm(1)*sigsq_om1
 
 !-------FIRST METHOD, DISCONTINUOUS SECOND DERIVATIVE
 
 !-------FIRST METHOD, DISCONTINUOUS SECOND DERIVATIVE
-        xm=0.5d0*(ssxm+ljxm)
-        do k=1,3
-          d_xm(k)=0.5d0*(d_ssxm(k)+d_ljxm(k))
-        enddo
-        if (rij.lt.xm) then
-          havebond=.true.
-          ssm=ssC-0.25D0*ssB*ssB/ssA
-          d_ssm(1)=0.5D0*akct*ssB/ssA
-          d_ssm(2)=2.0D0*akth*deltat2-om1*omega-d_ssm(1)
-          d_ssm(1)=-2.0D0*akth*deltat1-om2*omega+d_ssm(1)
-          d_ssm(3)=omega
-          f1=(rij-xm)/(ssxm-xm)
-          f2=(rij-ssxm)/(xm-ssxm)
-          h1=h_base(f1,hd1)
-          h2=h_base(f2,hd2)
-          eij=ssm*h1+Ht*h2
-          delta_inv=1.0d0/(xm-ssxm)
-          deltasq_inv=delta_inv*delta_inv
-          fac=ssm*hd1-Ht*hd2
-          fac1=deltasq_inv*fac*(xm-rij)
-          fac2=deltasq_inv*fac*(rij-ssxm)
-          ed=delta_inv*(Ht*hd2-ssm*hd1)
-          eom1=fac1*d_ssxm(1)+fac2*d_xm(1)+h1*d_ssm(1)
-          eom2=fac1*d_ssxm(2)+fac2*d_xm(2)+h1*d_ssm(2)
-          eom12=fac1*d_ssxm(3)+fac2*d_xm(3)+h1*d_ssm(3)
-        else
-          havebond=.false.
-          ljm=-0.25D0*ljB*bb_aq(itypi,itypj)/aa_aq(itypi,itypj)
-          d_ljm(1)=-0.5D0*bb_aq(itypi,itypj)/aa_aq(itypi,itypj)*ljB
-          d_ljm(2)=d_ljm(1)*(0.5D0*eps2rt_om2/eps2rt+alf2/eps3rt)
-          d_ljm(3)=d_ljm(1)*(0.5D0*eps1_om12+0.5D0*eps2rt_om12/eps2rt- &
-               alf12/eps3rt)
-          d_ljm(1)=d_ljm(1)*(0.5D0*eps2rt_om1/eps2rt-alf1/eps3rt)
-          f1=(rij-ljxm)/(xm-ljxm)
-          f2=(rij-xm)/(ljxm-xm)
-          h1=h_base(f1,hd1)
-          h2=h_base(f2,hd2)
-          eij=Ht*h1+ljm*h2
-          delta_inv=1.0d0/(ljxm-xm)
-          deltasq_inv=delta_inv*delta_inv
-          fac=Ht*hd1-ljm*hd2
-          fac1=deltasq_inv*fac*(ljxm-rij)
-          fac2=deltasq_inv*fac*(rij-xm)
-          ed=delta_inv*(ljm*hd2-Ht*hd1)
-          eom1=fac1*d_xm(1)+fac2*d_ljxm(1)+h2*d_ljm(1)
-          eom2=fac1*d_xm(2)+fac2*d_ljxm(2)+h2*d_ljm(2)
-          eom12=fac1*d_xm(3)+fac2*d_ljxm(3)+h2*d_ljm(3)
-        endif
+      xm=0.5d0*(ssxm+ljxm)
+      do k=1,3
+        d_xm(k)=0.5d0*(d_ssxm(k)+d_ljxm(k))
+      enddo
+      if (rij.lt.xm) then
+        havebond=.true.
+        ssm=ssC-0.25D0*ssB*ssB/ssA
+        d_ssm(1)=0.5D0*akct*ssB/ssA
+        d_ssm(2)=2.0D0*akth*deltat2-om1*omega-d_ssm(1)
+        d_ssm(1)=-2.0D0*akth*deltat1-om2*omega+d_ssm(1)
+        d_ssm(3)=omega
+        f1=(rij-xm)/(ssxm-xm)
+        f2=(rij-ssxm)/(xm-ssxm)
+        h1=h_base(f1,hd1)
+        h2=h_base(f2,hd2)
+        eij=ssm*h1+Ht*h2
+        delta_inv=1.0d0/(xm-ssxm)
+        deltasq_inv=delta_inv*delta_inv
+        fac=ssm*hd1-Ht*hd2
+        fac1=deltasq_inv*fac*(xm-rij)
+        fac2=deltasq_inv*fac*(rij-ssxm)
+        ed=delta_inv*(Ht*hd2-ssm*hd1)
+        eom1=fac1*d_ssxm(1)+fac2*d_xm(1)+h1*d_ssm(1)
+        eom2=fac1*d_ssxm(2)+fac2*d_xm(2)+h1*d_ssm(2)
+        eom12=fac1*d_ssxm(3)+fac2*d_xm(3)+h1*d_ssm(3)
+      else
+        havebond=.false.
+        ljm=-0.25D0*ljB*bb_aq(itypi,itypj)/aa_aq(itypi,itypj)
+        d_ljm(1)=-0.5D0*bb_aq(itypi,itypj)/aa_aq(itypi,itypj)*ljB
+        d_ljm(2)=d_ljm(1)*(0.5D0*eps2rt_om2/eps2rt+alf2/eps3rt)
+        d_ljm(3)=d_ljm(1)*(0.5D0*eps1_om12+0.5D0*eps2rt_om12/eps2rt- &
+             alf12/eps3rt)
+        d_ljm(1)=d_ljm(1)*(0.5D0*eps2rt_om1/eps2rt-alf1/eps3rt)
+        f1=(rij-ljxm)/(xm-ljxm)
+        f2=(rij-xm)/(ljxm-xm)
+        h1=h_base(f1,hd1)
+        h2=h_base(f2,hd2)
+        eij=Ht*h1+ljm*h2
+        delta_inv=1.0d0/(ljxm-xm)
+        deltasq_inv=delta_inv*delta_inv
+        fac=Ht*hd1-ljm*hd2
+        fac1=deltasq_inv*fac*(ljxm-rij)
+        fac2=deltasq_inv*fac*(rij-xm)
+        ed=delta_inv*(ljm*hd2-Ht*hd1)
+        eom1=fac1*d_xm(1)+fac2*d_ljxm(1)+h2*d_ljm(1)
+        eom2=fac1*d_xm(2)+fac2*d_ljxm(2)+h2*d_ljm(2)
+        eom12=fac1*d_xm(3)+fac2*d_ljxm(3)+h2*d_ljm(3)
+      endif
 !-------END FIRST METHOD, DISCONTINUOUS SECOND DERIVATIVE
 
 !-------SECOND METHOD, CONTINUOUS SECOND DERIVATIVE
 !-------END FIRST METHOD, DISCONTINUOUS SECOND DERIVATIVE
 
 !-------SECOND METHOD, CONTINUOUS SECOND DERIVATIVE
@@ -19017,9 +18739,9 @@
 !        endif
 !#endif
 !#endif
 !        endif
 !#endif
 !#endif
-        dyn_ssbond_ij(i,j)=eij
+      dyn_ssbond_ij(i,j)=eij
       else if (.not.havebond .and. dyn_ssbond_ij(i,j).lt.1.0d300) then
       else if (.not.havebond .and. dyn_ssbond_ij(i,j).lt.1.0d300) then
-        dyn_ssbond_ij(i,j)=1.0d300
+      dyn_ssbond_ij(i,j)=1.0d300
 !#ifndef CLUST
 !#ifndef WHAM
 !        write(iout,'(a15,f12.2,f8.1,2i5)')
 !#ifndef CLUST
 !#ifndef WHAM
 !        write(iout,'(a15,f12.2,f8.1,2i5)')
@@ -19030,35 +18752,35 @@
 
 !-------TESTING CODE
 !el      if (checkstop) then
 
 !-------TESTING CODE
 !el      if (checkstop) then
-        if (jcheck.eq.0) write(iout,'(a,3f15.8,$)') &
-             "CHECKSTOP",rij,eij,ed
-        echeck(jcheck)=eij
+      if (jcheck.eq.0) write(iout,'(a,3f15.8,$)') &
+           "CHECKSTOP",rij,eij,ed
+      echeck(jcheck)=eij
 !el      endif
       enddo
       if (checkstop) then
 !el      endif
       enddo
       if (checkstop) then
-        write(iout,'(f15.8)')(echeck(1)-echeck(-1))*0.5d0/deps
+      write(iout,'(f15.8)')(echeck(1)-echeck(-1))*0.5d0/deps
       endif
       enddo
       if (checkstop) then
       endif
       enddo
       if (checkstop) then
-        transgrad=.true.
-        checkstop=.false.
+      transgrad=.true.
+      checkstop=.false.
       endif
 !-------END TESTING CODE
 
       do k=1,3
       endif
 !-------END TESTING CODE
 
       do k=1,3
-        dcosom1(k)=(dc_norm(k,nres+i)-om1*erij(k))/rij
-        dcosom2(k)=(dc_norm(k,nres+j)-om2*erij(k))/rij
+      dcosom1(k)=(dc_norm(k,nres+i)-om1*erij(k))/rij
+      dcosom2(k)=(dc_norm(k,nres+j)-om2*erij(k))/rij
       enddo
       do k=1,3
       enddo
       do k=1,3
-        gg(k)=ed*erij(k)+eom1*dcosom1(k)+eom2*dcosom2(k)
+      gg(k)=ed*erij(k)+eom1*dcosom1(k)+eom2*dcosom2(k)
       enddo
       do k=1,3
       enddo
       do k=1,3
-        gvdwx(k,i)=gvdwx(k,i)-gg(k) &
-             +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
-             +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
-        gvdwx(k,j)=gvdwx(k,j)+gg(k) &
-             +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
-             +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+      gvdwx(k,i)=gvdwx(k,i)-gg(k) &
+           +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
+           +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+      gvdwx(k,j)=gvdwx(k,j)+gg(k) &
+           +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
+           +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
       enddo
 !grad      do k=i,j-1
 !grad        do l=1,3
       enddo
 !grad      do k=i,j-1
 !grad        do l=1,3
@@ -19067,14 +18789,14 @@
 !grad      enddo
 
       do l=1,3
 !grad      enddo
 
       do l=1,3
-        gvdwc(l,i)=gvdwc(l,i)-gg(l)
-        gvdwc(l,j)=gvdwc(l,j)+gg(l)
+      gvdwc(l,i)=gvdwc(l,i)-gg(l)
+      gvdwc(l,j)=gvdwc(l,j)+gg(l)
       enddo
 
       return
       end subroutine dyn_ssbond_ene
 !--------------------------------------------------------------------------
       enddo
 
       return
       end subroutine dyn_ssbond_ene
 !--------------------------------------------------------------------------
-         subroutine triple_ssbond_ene(resi,resj,resk,eij)
+       subroutine triple_ssbond_ene(resi,resj,resk,eij)
 !      implicit none
 !      Includes
       use calc_data
 !      implicit none
 !      Includes
       use calc_data
@@ -19132,11 +18854,12 @@
       xi=c(1,nres+i)
       yi=c(2,nres+i)
       zi=c(3,nres+i)
       xi=c(1,nres+i)
       yi=c(2,nres+i)
       zi=c(3,nres+i)
+      call to_box(xi,yi,zi)
       itypj=itype(j,1)
       xj=c(1,nres+j)
       yj=c(2,nres+j)
       zj=c(3,nres+j)
       itypj=itype(j,1)
       xj=c(1,nres+j)
       yj=c(2,nres+j)
       zj=c(3,nres+j)
-
+      call to_box(xj,yj,zj)
       dxj=dc_norm(1,nres+j)
       dyj=dc_norm(2,nres+j)
       dzj=dc_norm(3,nres+j)
       dxj=dc_norm(1,nres+j)
       dyj=dc_norm(2,nres+j)
       dzj=dc_norm(3,nres+j)
@@ -19145,7 +18868,7 @@
       xk=c(1,nres+k)
       yk=c(2,nres+k)
       zk=c(3,nres+k)
       xk=c(1,nres+k)
       yk=c(2,nres+k)
       zk=c(3,nres+k)
-
+       call to_box(xk,yk,zk)
       dxk=dc_norm(1,nres+k)
       dyk=dc_norm(2,nres+k)
       dzk=dc_norm(3,nres+k)
       dxk=dc_norm(1,nres+k)
       dyk=dc_norm(2,nres+k)
       dzk=dc_norm(3,nres+k)
@@ -19196,47 +18919,47 @@
 !C derivative over rij
       fac=-eij1**2/dtriss*(2.0*atriss*(rij-rik)+6.0*btriss*(rij+rik)**5) &
       -eij2**2/dtriss*(2.0*atriss*(rij-rjk)+6.0*btriss*(rij+rjk)**5)
 !C derivative over rij
       fac=-eij1**2/dtriss*(2.0*atriss*(rij-rik)+6.0*btriss*(rij+rik)**5) &
       -eij2**2/dtriss*(2.0*atriss*(rij-rjk)+6.0*btriss*(rij+rjk)**5)
-            gg(1)=xij*fac/rij
-            gg(2)=yij*fac/rij
-            gg(3)=zij*fac/rij
+          gg(1)=xij*fac/rij
+          gg(2)=yij*fac/rij
+          gg(3)=zij*fac/rij
       do m=1,3
       do m=1,3
-        gvdwx(m,i)=gvdwx(m,i)-gg(m)
-        gvdwx(m,j)=gvdwx(m,j)+gg(m)
+      gvdwx(m,i)=gvdwx(m,i)-gg(m)
+      gvdwx(m,j)=gvdwx(m,j)+gg(m)
       enddo
 
       do l=1,3
       enddo
 
       do l=1,3
-        gvdwc(l,i)=gvdwc(l,i)-gg(l)
-        gvdwc(l,j)=gvdwc(l,j)+gg(l)
+      gvdwc(l,i)=gvdwc(l,i)-gg(l)
+      gvdwc(l,j)=gvdwc(l,j)+gg(l)
       enddo
 !C now derivative over rik
       fac=-eij1**2/dtriss* &
       (-2.0*atriss*(rij-rik)+6.0*btriss*(rij+rik)**5) &
       -eij3**2/dtriss*(2.0*atriss*(rik-rjk)+6.0*btriss*(rik+rjk)**5)
       enddo
 !C now derivative over rik
       fac=-eij1**2/dtriss* &
       (-2.0*atriss*(rij-rik)+6.0*btriss*(rij+rik)**5) &
       -eij3**2/dtriss*(2.0*atriss*(rik-rjk)+6.0*btriss*(rik+rjk)**5)
-            gg(1)=xik*fac/rik
-            gg(2)=yik*fac/rik
-            gg(3)=zik*fac/rik
+          gg(1)=xik*fac/rik
+          gg(2)=yik*fac/rik
+          gg(3)=zik*fac/rik
       do m=1,3
       do m=1,3
-        gvdwx(m,i)=gvdwx(m,i)-gg(m)
-        gvdwx(m,k)=gvdwx(m,k)+gg(m)
+      gvdwx(m,i)=gvdwx(m,i)-gg(m)
+      gvdwx(m,k)=gvdwx(m,k)+gg(m)
       enddo
       do l=1,3
       enddo
       do l=1,3
-        gvdwc(l,i)=gvdwc(l,i)-gg(l)
-        gvdwc(l,k)=gvdwc(l,k)+gg(l)
+      gvdwc(l,i)=gvdwc(l,i)-gg(l)
+      gvdwc(l,k)=gvdwc(l,k)+gg(l)
       enddo
 !C now derivative over rjk
       fac=-eij2**2/dtriss* &
       (-2.0*atriss*(rij-rjk)+6.0*btriss*(rij+rjk)**5)- &
       eij3**2/dtriss*(-2.0*atriss*(rik-rjk)+6.0*btriss*(rik+rjk)**5)
       enddo
 !C now derivative over rjk
       fac=-eij2**2/dtriss* &
       (-2.0*atriss*(rij-rjk)+6.0*btriss*(rij+rjk)**5)- &
       eij3**2/dtriss*(-2.0*atriss*(rik-rjk)+6.0*btriss*(rik+rjk)**5)
-            gg(1)=xjk*fac/rjk
-            gg(2)=yjk*fac/rjk
-            gg(3)=zjk*fac/rjk
+          gg(1)=xjk*fac/rjk
+          gg(2)=yjk*fac/rjk
+          gg(3)=zjk*fac/rjk
       do m=1,3
       do m=1,3
-        gvdwx(m,j)=gvdwx(m,j)-gg(m)
-        gvdwx(m,k)=gvdwx(m,k)+gg(m)
+      gvdwx(m,j)=gvdwx(m,j)-gg(m)
+      gvdwx(m,k)=gvdwx(m,k)+gg(m)
       enddo
       do l=1,3
       enddo
       do l=1,3
-        gvdwc(l,j)=gvdwc(l,j)-gg(l)
-        gvdwc(l,k)=gvdwc(l,k)+gg(l)
+      gvdwc(l,j)=gvdwc(l,j)-gg(l)
+      gvdwc(l,k)=gvdwc(l,k)+gg(l)
       enddo
       return
       end subroutine triple_ssbond_ene
       enddo
       return
       end subroutine triple_ssbond_ene
@@ -19302,7 +19025,7 @@
       integer :: i,j,imin,ierr
       integer :: diff,allnss,newnss
       integer,dimension(maxdim) :: allflag,allihpb,alljhpb,& !(maxdim)(maxdim=(maxres-1)*(maxres-2)/2)
       integer :: i,j,imin,ierr
       integer :: diff,allnss,newnss
       integer,dimension(maxdim) :: allflag,allihpb,alljhpb,& !(maxdim)(maxdim=(maxres-1)*(maxres-2)/2)
-                newihpb,newjhpb
+            newihpb,newjhpb
       logical :: found
       integer,dimension(0:nfgtasks) :: i_newnss
       integer,dimension(0:nfgtasks) :: displ
       logical :: found
       integer,dimension(0:nfgtasks) :: i_newnss
       integer,dimension(0:nfgtasks) :: displ
@@ -19311,78 +19034,78 @@
 
       allnss=0
       do i=1,nres-1
 
       allnss=0
       do i=1,nres-1
-        do j=i+1,nres
-          if (dyn_ssbond_ij(i,j).lt.1.0d300) then
-            allnss=allnss+1
-            allflag(allnss)=0
-            allihpb(allnss)=i
-            alljhpb(allnss)=j
-          endif
-        enddo
+      do j=i+1,nres
+        if (dyn_ssbond_ij(i,j).lt.1.0d300) then
+          allnss=allnss+1
+          allflag(allnss)=0
+          allihpb(allnss)=i
+          alljhpb(allnss)=j
+        endif
+      enddo
       enddo
 
 !mc      write(iout,*)"ALLNSS ",allnss,(allihpb(i),alljhpb(i),i=1,allnss)
 
  1    emin=1.0d300
       do i=1,allnss
       enddo
 
 !mc      write(iout,*)"ALLNSS ",allnss,(allihpb(i),alljhpb(i),i=1,allnss)
 
  1    emin=1.0d300
       do i=1,allnss
+      if (allflag(i).eq.0 .and. &
+           dyn_ssbond_ij(allihpb(i),alljhpb(i)).lt.emin) then
+        emin=dyn_ssbond_ij(allihpb(i),alljhpb(i))
+        imin=i
+      endif
+      enddo
+      if (emin.lt.1.0d300) then
+      allflag(imin)=1
+      do i=1,allnss
         if (allflag(i).eq.0 .and. &
         if (allflag(i).eq.0 .and. &
-             dyn_ssbond_ij(allihpb(i),alljhpb(i)).lt.emin) then
-          emin=dyn_ssbond_ij(allihpb(i),alljhpb(i))
-          imin=i
+             (allihpb(i).eq.allihpb(imin) .or. &
+             alljhpb(i).eq.allihpb(imin) .or. &
+             allihpb(i).eq.alljhpb(imin) .or. &
+             alljhpb(i).eq.alljhpb(imin))) then
+          allflag(i)=-1
         endif
       enddo
         endif
       enddo
-      if (emin.lt.1.0d300) then
-        allflag(imin)=1
-        do i=1,allnss
-          if (allflag(i).eq.0 .and. &
-               (allihpb(i).eq.allihpb(imin) .or. &
-               alljhpb(i).eq.allihpb(imin) .or. &
-               allihpb(i).eq.alljhpb(imin) .or. &
-               alljhpb(i).eq.alljhpb(imin))) then
-            allflag(i)=-1
-          endif
-        enddo
-        goto 1
+      goto 1
       endif
 
 !mc      write(iout,*)"ALLNSS ",allnss,(allihpb(i),alljhpb(i),i=1,allnss)
 
       newnss=0
       do i=1,allnss
       endif
 
 !mc      write(iout,*)"ALLNSS ",allnss,(allihpb(i),alljhpb(i),i=1,allnss)
 
       newnss=0
       do i=1,allnss
-        if (allflag(i).eq.1) then
-          newnss=newnss+1
-          newihpb(newnss)=allihpb(i)
-          newjhpb(newnss)=alljhpb(i)
-        endif
+      if (allflag(i).eq.1) then
+        newnss=newnss+1
+        newihpb(newnss)=allihpb(i)
+        newjhpb(newnss)=alljhpb(i)
+      endif
       enddo
 
 #ifdef MPI
       if (nfgtasks.gt.1)then
 
       enddo
 
 #ifdef MPI
       if (nfgtasks.gt.1)then
 
-        call MPI_Reduce(newnss,g_newnss,1,&
-          MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
-        call MPI_Gather(newnss,1,MPI_INTEGER,&
-                        i_newnss,1,MPI_INTEGER,king,FG_COMM,IERR)
-        displ(0)=0
-        do i=1,nfgtasks-1,1
-          displ(i)=i_newnss(i-1)+displ(i-1)
-        enddo
-        call MPI_Gatherv(newihpb,newnss,MPI_INTEGER,&
-                         g_newihpb,i_newnss,displ,MPI_INTEGER,&
-                         king,FG_COMM,IERR)     
-        call MPI_Gatherv(newjhpb,newnss,MPI_INTEGER,&
-                         g_newjhpb,i_newnss,displ,MPI_INTEGER,&
-                         king,FG_COMM,IERR)     
-        if(fg_rank.eq.0) then
+      call MPI_Reduce(newnss,g_newnss,1,&
+        MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
+      call MPI_Gather(newnss,1,MPI_INTEGER,&
+                  i_newnss,1,MPI_INTEGER,king,FG_COMM,IERR)
+      displ(0)=0
+      do i=1,nfgtasks-1,1
+        displ(i)=i_newnss(i-1)+displ(i-1)
+      enddo
+      call MPI_Gatherv(newihpb,newnss,MPI_INTEGER,&
+                   g_newihpb,i_newnss,displ,MPI_INTEGER,&
+                   king,FG_COMM,IERR)     
+      call MPI_Gatherv(newjhpb,newnss,MPI_INTEGER,&
+                   g_newjhpb,i_newnss,displ,MPI_INTEGER,&
+                   king,FG_COMM,IERR)     
+      if(fg_rank.eq.0) then
 !         print *,'g_newnss',g_newnss
 !         print *,'g_newihpb',(g_newihpb(i),i=1,g_newnss)
 !         print *,'g_newjhpb',(g_newjhpb(i),i=1,g_newnss)
 !         print *,'g_newnss',g_newnss
 !         print *,'g_newihpb',(g_newihpb(i),i=1,g_newnss)
 !         print *,'g_newjhpb',(g_newjhpb(i),i=1,g_newnss)
-         newnss=g_newnss  
-         do i=1,newnss
-          newihpb(i)=g_newihpb(i)
-          newjhpb(i)=g_newjhpb(i)
-         enddo
-        endif
+       newnss=g_newnss  
+       do i=1,newnss
+        newihpb(i)=g_newihpb(i)
+        newjhpb(i)=g_newjhpb(i)
+       enddo
+      endif
       endif
 #endif
 
       endif
 #endif
 
@@ -19391,45 +19114,44 @@
 !mc      write(iout,*)"NEWNSS ",newnss,(newihpb(i),newjhpb(i),i=1,newnss)
 !       print *,newnss,nss,maxdim
       do i=1,nss
 !mc      write(iout,*)"NEWNSS ",newnss,(newihpb(i),newjhpb(i),i=1,newnss)
 !       print *,newnss,nss,maxdim
       do i=1,nss
-        found=.false.
+      found=.false.
 !        print *,newnss
 !        print *,newnss
-        do j=1,newnss
+      do j=1,newnss
 !!          print *,j
 !!          print *,j
-          if (idssb(i).eq.newihpb(j) .and. &
-               jdssb(i).eq.newjhpb(j)) found=.true.
-        enddo
-#ifndef CLUST
-#ifndef WHAM
+        if (idssb(i).eq.newihpb(j) .and. &
+             jdssb(i).eq.newjhpb(j)) found=.true.
+      enddo
+#if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
 !        write(iout,*) "found",found,i,j
 !        write(iout,*) "found",found,i,j
-        if (.not.found.and.fg_rank.eq.0) &
-            write(iout,'(a15,f12.2,f8.1,2i5)') &
-             "SSBOND_BREAK",totT,t_bath,idssb(i),jdssb(i)
-#endif
+      if (.not.found.and.fg_rank.eq.0) &
+          write(iout,'(a15,f12.2,f8.1,2i5)') &
+           "SSBOND_BREAK",totT,t_bath,idssb(i),jdssb(i)
 #endif
       enddo
 
       do i=1,newnss
 #endif
       enddo
 
       do i=1,newnss
-        found=.false.
-        do j=1,nss
+      found=.false.
+      do j=1,nss
 !          print *,i,j
 !          print *,i,j
-          if (newihpb(i).eq.idssb(j) .and. &
-               newjhpb(i).eq.jdssb(j)) found=.true.
-        enddo
-#ifndef CLUST
-#ifndef WHAM
+        if (newihpb(i).eq.idssb(j) .and. &
+             newjhpb(i).eq.jdssb(j)) found=.true.
+      enddo
+#if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
 !        write(iout,*) "found",found,i,j
 !        write(iout,*) "found",found,i,j
-        if (.not.found.and.fg_rank.eq.0) &
-            write(iout,'(a15,f12.2,f8.1,2i5)') &
-             "SSBOND_FORM",totT,t_bath,newihpb(i),newjhpb(i)
-#endif
+      if (.not.found.and.fg_rank.eq.0) &
+          write(iout,'(a15,f12.2,f8.1,2i5)') &
+           "SSBOND_FORM",totT,t_bath,newihpb(i),newjhpb(i)
 #endif
       enddo
 #endif
       enddo
-
+!#if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
       nss=newnss
       do i=1,nss
       nss=newnss
       do i=1,nss
-        idssb(i)=newihpb(i)
-        jdssb(i)=newjhpb(i)
+      idssb(i)=newihpb(i)
+      jdssb(i)=newjhpb(i)
       enddo
       enddo
+!#else
+!      nss=0
+!#endif
 
       return
       end subroutine dyn_set_nss
 
       return
       end subroutine dyn_set_nss
@@ -19450,45 +19172,45 @@
 !      print *, "I am in eliptran"
       do i=ilip_start,ilip_end
 !C       do i=1,1
 !      print *, "I am in eliptran"
       do i=ilip_start,ilip_end
 !C       do i=1,1
-        if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1).or.(i.eq.nres))&
-         cycle
+      if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1).or.(i.eq.nres))&
+       cycle
 
 
-        positi=(mod(((c(3,i)+c(3,i+1))/2.0d0),boxzsize))
-        if (positi.le.0.0) positi=positi+boxzsize
+      positi=(mod(((c(3,i)+c(3,i+1))/2.0d0),boxzsize))
+      if (positi.le.0.0) positi=positi+boxzsize
 !C        print *,i
 !C first for peptide groups
 !c for each residue check if it is in lipid or lipid water border area
        if ((positi.gt.bordlipbot)  &
       .and.(positi.lt.bordliptop)) then
 !C the energy transfer exist
 !C        print *,i
 !C first for peptide groups
 !c for each residue check if it is in lipid or lipid water border area
        if ((positi.gt.bordlipbot)  &
       .and.(positi.lt.bordliptop)) then
 !C the energy transfer exist
-        if (positi.lt.buflipbot) then
+      if (positi.lt.buflipbot) then
 !C what fraction I am in
 !C what fraction I am in
-         fracinbuf=1.0d0-      &
-             ((positi-bordlipbot)/lipbufthick)
+       fracinbuf=1.0d0-      &
+           ((positi-bordlipbot)/lipbufthick)
 !C lipbufthick is thickenes of lipid buffore
 !C lipbufthick is thickenes of lipid buffore
-         sslip=sscalelip(fracinbuf)
-         ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
-         eliptran=eliptran+sslip*pepliptran
-         gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
-         gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
+       sslip=sscalelip(fracinbuf)
+       ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
+       eliptran=eliptran+sslip*pepliptran
+       gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
+       gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
 !C         gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
 
 !C        print *,"doing sccale for lower part"
 !C         print *,i,sslip,fracinbuf,ssgradlip
 !C         gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
 
 !C        print *,"doing sccale for lower part"
 !C         print *,i,sslip,fracinbuf,ssgradlip
-        elseif (positi.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
-         sslip=sscalelip(fracinbuf)
-         ssgradlip=sscagradlip(fracinbuf)/lipbufthick
-         eliptran=eliptran+sslip*pepliptran
-         gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
-         gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
+      elseif (positi.gt.bufliptop) then
+       fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+       sslip=sscalelip(fracinbuf)
+       ssgradlip=sscagradlip(fracinbuf)/lipbufthick
+       eliptran=eliptran+sslip*pepliptran
+       gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
+       gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
 !C         gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
 !C          print *, "doing sscalefor top part"
 !C         print *,i,sslip,fracinbuf,ssgradlip
 !C         gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
 !C          print *, "doing sscalefor top part"
 !C         print *,i,sslip,fracinbuf,ssgradlip
-        else
-         eliptran=eliptran+pepliptran
+      else
+       eliptran=eliptran+pepliptran
 !C         print *,"I am in true lipid"
 !C         print *,"I am in true lipid"
-        endif
+      endif
 !C       else
 !C       eliptran=elpitran+0.0 ! I am in water
        endif
 !C       else
 !C       eliptran=elpitran+0.0 ! I am in water
        endif
@@ -19496,9 +19218,9 @@
        enddo
 ! here starts the side chain transfer
        do i=ilip_start,ilip_end
        enddo
 ! here starts the side chain transfer
        do i=ilip_start,ilip_end
-        if (itype(i,1).eq.ntyp1) cycle
-        positi=(mod(c(3,i+nres),boxzsize))
-        if (positi.le.0) positi=positi+boxzsize
+      if (itype(i,1).eq.ntyp1) cycle
+      positi=(mod(c(3,i+nres),boxzsize))
+      if (positi.le.0) positi=positi+boxzsize
 !C       print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
 !c for each residue check if it is in lipid or lipid water border area
 !C       respos=mod(c(3,i+nres),boxzsize)
 !C       print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
 !c for each residue check if it is in lipid or lipid water border area
 !C       respos=mod(c(3,i+nres),boxzsize)
@@ -19506,37 +19228,37 @@
        if ((positi.gt.bordlipbot) &
        .and.(positi.lt.bordliptop)) then
 !C the energy transfer exist
        if ((positi.gt.bordlipbot) &
        .and.(positi.lt.bordliptop)) then
 !C the energy transfer exist
-        if (positi.lt.buflipbot) then
-         fracinbuf=1.0d0-   &
-           ((positi-bordlipbot)/lipbufthick)
+      if (positi.lt.buflipbot) then
+       fracinbuf=1.0d0-   &
+         ((positi-bordlipbot)/lipbufthick)
 !C lipbufthick is thickenes of lipid buffore
 !C lipbufthick is thickenes of lipid buffore
-         sslip=sscalelip(fracinbuf)
-         ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
-         eliptran=eliptran+sslip*liptranene(itype(i,1))
-         gliptranx(3,i)=gliptranx(3,i) &
+       sslip=sscalelip(fracinbuf)
+       ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
+       eliptran=eliptran+sslip*liptranene(itype(i,1))
+       gliptranx(3,i)=gliptranx(3,i) &
       +ssgradlip*liptranene(itype(i,1))
       +ssgradlip*liptranene(itype(i,1))
-         gliptranc(3,i-1)= gliptranc(3,i-1) &
+       gliptranc(3,i-1)= gliptranc(3,i-1) &
       +ssgradlip*liptranene(itype(i,1))
 !C         print *,"doing sccale for lower part"
       +ssgradlip*liptranene(itype(i,1))
 !C         print *,"doing sccale for lower part"
-        elseif (positi.gt.bufliptop) then
-         fracinbuf=1.0d0-  &
+      elseif (positi.gt.bufliptop) then
+       fracinbuf=1.0d0-  &
       ((bordliptop-positi)/lipbufthick)
       ((bordliptop-positi)/lipbufthick)
-         sslip=sscalelip(fracinbuf)
-         ssgradlip=sscagradlip(fracinbuf)/lipbufthick
-         eliptran=eliptran+sslip*liptranene(itype(i,1))
-         gliptranx(3,i)=gliptranx(3,i)  &
+       sslip=sscalelip(fracinbuf)
+       ssgradlip=sscagradlip(fracinbuf)/lipbufthick
+       eliptran=eliptran+sslip*liptranene(itype(i,1))
+       gliptranx(3,i)=gliptranx(3,i)  &
        +ssgradlip*liptranene(itype(i,1))
        +ssgradlip*liptranene(itype(i,1))
-         gliptranc(3,i-1)= gliptranc(3,i-1) &
+       gliptranc(3,i-1)= gliptranc(3,i-1) &
       +ssgradlip*liptranene(itype(i,1))
 !C          print *, "doing sscalefor top part",sslip,fracinbuf
       +ssgradlip*liptranene(itype(i,1))
 !C          print *, "doing sscalefor top part",sslip,fracinbuf
-        else
-         eliptran=eliptran+liptranene(itype(i,1))
+      else
+       eliptran=eliptran+liptranene(itype(i,1))
 !C         print *,"I am in true lipid"
 !C         print *,"I am in true lipid"
-        endif
-        endif ! if in lipid or buffor
+      endif
+      endif ! if in lipid or buffor
 !C       else
 !C       eliptran=elpitran+0.0 ! I am in water
 !C       else
 !C       eliptran=elpitran+0.0 ! I am in water
-        if (energy_dec) write(iout,*) i,"eliptran=",eliptran
+      if (energy_dec) write(iout,*) i,"eliptran=",eliptran
        enddo
        return
        end  subroutine Eliptransfer
        enddo
        return
        end  subroutine Eliptransfer
@@ -19560,8 +19282,8 @@
       integer :: i,j,iti
       Etube=0.0d0
       do i=itube_start,itube_end
       integer :: i,j,iti
       Etube=0.0d0
       do i=itube_start,itube_end
-        enetube(i)=0.0d0
-        enetube(i+nres)=0.0d0
+      enetube(i)=0.0d0
+      enetube(i+nres)=0.0d0
       enddo
 !C first we calculate the distance from tube center
 !C for UNRES
       enddo
 !C first we calculate the distance from tube center
 !C for UNRES
@@ -19572,22 +19294,22 @@
       xmin=boxxsize
       ymin=boxysize
 ! Find minimum distance in periodic box
       xmin=boxxsize
       ymin=boxysize
 ! Find minimum distance in periodic box
-        do j=-1,1
-         vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
-         vectube(1)=vectube(1)+boxxsize*j
-         vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
-         vectube(2)=vectube(2)+boxysize*j
-         xminact=abs(vectube(1)-tubecenter(1))
-         yminact=abs(vectube(2)-tubecenter(2))
-           if (xmin.gt.xminact) then
-            xmin=xminact
-            xtemp=vectube(1)
-           endif
-           if (ymin.gt.yminact) then
-             ymin=yminact
-             ytemp=vectube(2)
-            endif
-         enddo
+      do j=-1,1
+       vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+       vectube(1)=vectube(1)+boxxsize*j
+       vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+       vectube(2)=vectube(2)+boxysize*j
+       xminact=abs(vectube(1)-tubecenter(1))
+       yminact=abs(vectube(2)-tubecenter(2))
+         if (xmin.gt.xminact) then
+          xmin=xminact
+          xtemp=vectube(1)
+         endif
+         if (ymin.gt.yminact) then
+           ymin=yminact
+           ytemp=vectube(2)
+          endif
+       enddo
       vectube(1)=xtemp
       vectube(2)=ytemp
       vectube(1)=vectube(1)-tubecenter(1)
       vectube(1)=xtemp
       vectube(2)=ytemp
       vectube(1)=vectube(1)-tubecenter(1)
@@ -19615,46 +19337,46 @@
 !C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
 !C now we calculate gradient
        fac=(-12.0d0*pep_aa_tube/rdiff6- &
 !C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
 !C now we calculate gradient
        fac=(-12.0d0*pep_aa_tube/rdiff6- &
-            6.0d0*pep_bb_tube)/rdiff6/rdiff
+          6.0d0*pep_bb_tube)/rdiff6/rdiff
 !C       write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
 !C     &rdiff,fac
 !C now direction of gg_tube vector
 !C       write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
 !C     &rdiff,fac
 !C now direction of gg_tube vector
-        do j=1,3
-        gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
-        gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0
-        enddo
-        enddo
+      do j=1,3
+      gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
+      gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0
+      enddo
+      enddo
 !C basically thats all code now we split for side-chains (REMEMBER to sum up at the END)
 !C        print *,gg_tube(1,0),"TU"
 
 
        do i=itube_start,itube_end
 !C Lets not jump over memory as we use many times iti
 !C basically thats all code now we split for side-chains (REMEMBER to sum up at the END)
 !C        print *,gg_tube(1,0),"TU"
 
 
        do i=itube_start,itube_end
 !C Lets not jump over memory as we use many times iti
-         iti=itype(i,1)
+       iti=itype(i,1)
 !C lets ommit dummy atoms for now
 !C lets ommit dummy atoms for now
-         if ((iti.eq.ntyp1)  &
+       if ((iti.eq.ntyp1)  &
 !C in UNRES uncomment the line below as GLY has no side-chain...
 !C      .or.(iti.eq.10)
 !C in UNRES uncomment the line below as GLY has no side-chain...
 !C      .or.(iti.eq.10)
-        ) cycle
+      ) cycle
       xmin=boxxsize
       ymin=boxysize
       xmin=boxxsize
       ymin=boxysize
-        do j=-1,1
-         vectube(1)=mod((c(1,i+nres)),boxxsize)
-         vectube(1)=vectube(1)+boxxsize*j
-         vectube(2)=mod((c(2,i+nres)),boxysize)
-         vectube(2)=vectube(2)+boxysize*j
-
-         xminact=abs(vectube(1)-tubecenter(1))
-         yminact=abs(vectube(2)-tubecenter(2))
-           if (xmin.gt.xminact) then
-            xmin=xminact
-            xtemp=vectube(1)
-           endif
-           if (ymin.gt.yminact) then
-             ymin=yminact
-             ytemp=vectube(2)
-            endif
-         enddo
+      do j=-1,1
+       vectube(1)=mod((c(1,i+nres)),boxxsize)
+       vectube(1)=vectube(1)+boxxsize*j
+       vectube(2)=mod((c(2,i+nres)),boxysize)
+       vectube(2)=vectube(2)+boxysize*j
+
+       xminact=abs(vectube(1)-tubecenter(1))
+       yminact=abs(vectube(2)-tubecenter(2))
+         if (xmin.gt.xminact) then
+          xmin=xminact
+          xtemp=vectube(1)
+         endif
+         if (ymin.gt.yminact) then
+           ymin=yminact
+           ytemp=vectube(2)
+          endif
+       enddo
       vectube(1)=xtemp
       vectube(2)=ytemp
 !C          write(iout,*), "tututu", vectube(1),tubecenter(1),vectube(2),
       vectube(1)=xtemp
       vectube(2)=ytemp
 !C          write(iout,*), "tututu", vectube(1),tubecenter(1),vectube(2),
@@ -19680,19 +19402,19 @@
        sc_bb_tube=sc_bb_tube_par(iti)
        enetube(i+nres)=sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6
        fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff-  &
        sc_bb_tube=sc_bb_tube_par(iti)
        enetube(i+nres)=sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6
        fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff-  &
-             6.0d0*sc_bb_tube/rdiff6/rdiff
+           6.0d0*sc_bb_tube/rdiff6/rdiff
 !C now direction of gg_tube vector
 !C now direction of gg_tube vector
-         do j=1,3
-          gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac
-          gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
-         enddo
-        enddo
-        do i=itube_start,itube_end
-          Etube=Etube+enetube(i)+enetube(i+nres)
-        enddo
+       do j=1,3
+        gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac
+        gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
+       enddo
+      enddo
+      do i=itube_start,itube_end
+        Etube=Etube+enetube(i)+enetube(i+nres)
+      enddo
 !C        print *,"ETUBE", etube
 !C        print *,"ETUBE", etube
-        return
-        end subroutine calctube
+      return
+      end subroutine calctube
 !C TO DO 1) add to total energy
 !C       2) add to gradient summation
 !C       3) add reading parameters (AND of course oppening of PARAM file)
 !C TO DO 1) add to total energy
 !C       2) add to gradient summation
 !C       3) add reading parameters (AND of course oppening of PARAM file)
@@ -19714,15 +19436,15 @@
 !C and r0 is the excluded size of nanotube (can be set to 0 if we want just a 
 !C simple Kihara potential
       subroutine calctube2(Etube)
 !C and r0 is the excluded size of nanotube (can be set to 0 if we want just a 
 !C simple Kihara potential
       subroutine calctube2(Etube)
-            real(kind=8),dimension(3) :: vectube
+          real(kind=8),dimension(3) :: vectube
       real(kind=8) :: Etube,xtemp,xminact,yminact,&
        ytemp,xmin,ymin,tub_r,rdiff,rdiff6,fac,positi,fracinbuf,&
        sstube,ssgradtube,sc_aa_tube,sc_bb_tube
       integer:: i,j,iti
       Etube=0.0d0
       do i=itube_start,itube_end
       real(kind=8) :: Etube,xtemp,xminact,yminact,&
        ytemp,xmin,ymin,tub_r,rdiff,rdiff6,fac,positi,fracinbuf,&
        sstube,ssgradtube,sc_aa_tube,sc_bb_tube
       integer:: i,j,iti
       Etube=0.0d0
       do i=itube_start,itube_end
-        enetube(i)=0.0d0
-        enetube(i+nres)=0.0d0
+      enetube(i)=0.0d0
+      enetube(i+nres)=0.0d0
       enddo
 !C first we calculate the distance from tube center
 !C first sugare-phosphate group for NARES this would be peptide group 
       enddo
 !C first we calculate the distance from tube center
 !C first sugare-phosphate group for NARES this would be peptide group 
@@ -19738,23 +19460,23 @@
 !C          if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
       xmin=boxxsize
       ymin=boxysize
 !C          if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
       xmin=boxxsize
       ymin=boxysize
-        do j=-1,1
-         vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
-         vectube(1)=vectube(1)+boxxsize*j
-         vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
-         vectube(2)=vectube(2)+boxysize*j
-
-         xminact=abs(vectube(1)-tubecenter(1))
-         yminact=abs(vectube(2)-tubecenter(2))
-           if (xmin.gt.xminact) then
-            xmin=xminact
-            xtemp=vectube(1)
-           endif
-           if (ymin.gt.yminact) then
-             ymin=yminact
-             ytemp=vectube(2)
-            endif
-         enddo
+      do j=-1,1
+       vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+       vectube(1)=vectube(1)+boxxsize*j
+       vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+       vectube(2)=vectube(2)+boxysize*j
+
+       xminact=abs(vectube(1)-tubecenter(1))
+       yminact=abs(vectube(2)-tubecenter(2))
+         if (xmin.gt.xminact) then
+          xmin=xminact
+          xtemp=vectube(1)
+         endif
+         if (ymin.gt.yminact) then
+           ymin=yminact
+           ytemp=vectube(2)
+          endif
+       enddo
       vectube(1)=xtemp
       vectube(2)=ytemp
       vectube(1)=vectube(1)-tubecenter(1)
       vectube(1)=xtemp
       vectube(2)=ytemp
       vectube(1)=vectube(1)-tubecenter(1)
@@ -19776,140 +19498,140 @@
 !C and its 6 power
       rdiff6=rdiff**6.0d0
 !C THIS FRAGMENT MAKES TUBE FINITE
 !C and its 6 power
       rdiff6=rdiff**6.0d0
 !C THIS FRAGMENT MAKES TUBE FINITE
-        positi=mod((c(3,i)+c(3,i+1))/2.0d0,boxzsize)
-        if (positi.le.0) positi=positi+boxzsize
+      positi=mod((c(3,i)+c(3,i+1))/2.0d0,boxzsize)
+      if (positi.le.0) positi=positi+boxzsize
 !C       print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
 !c for each residue check if it is in lipid or lipid water border area
 !C       respos=mod(c(3,i+nres),boxzsize)
 !C       print *,positi,bordtubebot,buftubebot,bordtubetop
        if ((positi.gt.bordtubebot)  &
 !C       print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
 !c for each residue check if it is in lipid or lipid water border area
 !C       respos=mod(c(3,i+nres),boxzsize)
 !C       print *,positi,bordtubebot,buftubebot,bordtubetop
        if ((positi.gt.bordtubebot)  &
-        .and.(positi.lt.bordtubetop)) then
+      .and.(positi.lt.bordtubetop)) then
 !C the energy transfer exist
 !C the energy transfer exist
-        if (positi.lt.buftubebot) then
-         fracinbuf=1.0d0-  &
-           ((positi-bordtubebot)/tubebufthick)
+      if (positi.lt.buftubebot) then
+       fracinbuf=1.0d0-  &
+         ((positi-bordtubebot)/tubebufthick)
 !C lipbufthick is thickenes of lipid buffore
 !C lipbufthick is thickenes of lipid buffore
-         sstube=sscalelip(fracinbuf)
-         ssgradtube=-sscagradlip(fracinbuf)/tubebufthick
+       sstube=sscalelip(fracinbuf)
+       ssgradtube=-sscagradlip(fracinbuf)/tubebufthick
 !C         print *,ssgradtube, sstube,tubetranene(itype(i,1))
 !C         print *,ssgradtube, sstube,tubetranene(itype(i,1))
-         enetube(i)=enetube(i)+sstube*tubetranenepep
+       enetube(i)=enetube(i)+sstube*tubetranenepep
 !C         gg_tube_SC(3,i)=gg_tube_SC(3,i)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C         gg_tube(3,i-1)= gg_tube(3,i-1)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C         print *,"doing sccale for lower part"
 !C         gg_tube_SC(3,i)=gg_tube_SC(3,i)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C         gg_tube(3,i-1)= gg_tube(3,i-1)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C         print *,"doing sccale for lower part"
-        elseif (positi.gt.buftubetop) then
-         fracinbuf=1.0d0-  &
-        ((bordtubetop-positi)/tubebufthick)
-         sstube=sscalelip(fracinbuf)
-         ssgradtube=sscagradlip(fracinbuf)/tubebufthick
-         enetube(i)=enetube(i)+sstube*tubetranenepep
+      elseif (positi.gt.buftubetop) then
+       fracinbuf=1.0d0-  &
+      ((bordtubetop-positi)/tubebufthick)
+       sstube=sscalelip(fracinbuf)
+       ssgradtube=sscagradlip(fracinbuf)/tubebufthick
+       enetube(i)=enetube(i)+sstube*tubetranenepep
 !C         gg_tube_SC(3,i)=gg_tube_SC(3,i)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C         gg_tube(3,i-1)= gg_tube(3,i-1)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C          print *, "doing sscalefor top part",sslip,fracinbuf
 !C         gg_tube_SC(3,i)=gg_tube_SC(3,i)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C         gg_tube(3,i-1)= gg_tube(3,i-1)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C          print *, "doing sscalefor top part",sslip,fracinbuf
-        else
-         sstube=1.0d0
-         ssgradtube=0.0d0
-         enetube(i)=enetube(i)+sstube*tubetranenepep
+      else
+       sstube=1.0d0
+       ssgradtube=0.0d0
+       enetube(i)=enetube(i)+sstube*tubetranenepep
 !C         print *,"I am in true lipid"
 !C         print *,"I am in true lipid"
-        endif
-        else
+      endif
+      else
 !C          sstube=0.0d0
 !C          ssgradtube=0.0d0
 !C          sstube=0.0d0
 !C          ssgradtube=0.0d0
-        cycle
-        endif ! if in lipid or buffor
+      cycle
+      endif ! if in lipid or buffor
 
 !C for vectorization reasons we will sumup at the end to avoid depenence of previous
        enetube(i)=enetube(i)+sstube* &
 
 !C for vectorization reasons we will sumup at the end to avoid depenence of previous
        enetube(i)=enetube(i)+sstube* &
-        (pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6)
+      (pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6)
 !C       write(iout,*) "TU13",i,rdiff6,enetube(i)
 !C       print *,rdiff,rdiff6,pep_aa_tube
 !C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
 !C now we calculate gradient
        fac=(-12.0d0*pep_aa_tube/rdiff6-  &
 !C       write(iout,*) "TU13",i,rdiff6,enetube(i)
 !C       print *,rdiff,rdiff6,pep_aa_tube
 !C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
 !C now we calculate gradient
        fac=(-12.0d0*pep_aa_tube/rdiff6-  &
-             6.0d0*pep_bb_tube)/rdiff6/rdiff*sstube
+           6.0d0*pep_bb_tube)/rdiff6/rdiff*sstube
 !C       write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
 !C     &rdiff,fac
 
 !C now direction of gg_tube vector
        do j=1,3
 !C       write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
 !C     &rdiff,fac
 
 !C now direction of gg_tube vector
        do j=1,3
-        gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
-        gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0
-        enddo
-         gg_tube(3,i)=gg_tube(3,i)  &
+      gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
+      gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0
+      enddo
+       gg_tube(3,i)=gg_tube(3,i)  &
        +ssgradtube*enetube(i)/sstube/2.0d0
        +ssgradtube*enetube(i)/sstube/2.0d0
-         gg_tube(3,i-1)= gg_tube(3,i-1)  &
+       gg_tube(3,i-1)= gg_tube(3,i-1)  &
        +ssgradtube*enetube(i)/sstube/2.0d0
 
        +ssgradtube*enetube(i)/sstube/2.0d0
 
-        enddo
+      enddo
 !C basically thats all code now we split for side-chains (REMEMBER to sum up at the END)
 !C        print *,gg_tube(1,0),"TU"
 !C basically thats all code now we split for side-chains (REMEMBER to sum up at the END)
 !C        print *,gg_tube(1,0),"TU"
-        do i=itube_start,itube_end
+      do i=itube_start,itube_end
 !C Lets not jump over memory as we use many times iti
 !C Lets not jump over memory as we use many times iti
-         iti=itype(i,1)
+       iti=itype(i,1)
 !C lets ommit dummy atoms for now
 !C lets ommit dummy atoms for now
-         if ((iti.eq.ntyp1) &
+       if ((iti.eq.ntyp1) &
 !!C in UNRES uncomment the line below as GLY has no side-chain...
 !!C in UNRES uncomment the line below as GLY has no side-chain...
-           .or.(iti.eq.10) &
-          ) cycle
-          vectube(1)=c(1,i+nres)
-          vectube(1)=mod(vectube(1),boxxsize)
-          if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
-          vectube(2)=c(2,i+nres)
-          vectube(2)=mod(vectube(2),boxysize)
-          if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
+         .or.(iti.eq.10) &
+        ) cycle
+        vectube(1)=c(1,i+nres)
+        vectube(1)=mod(vectube(1),boxxsize)
+        if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
+        vectube(2)=c(2,i+nres)
+        vectube(2)=mod(vectube(2),boxysize)
+        if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
 
       vectube(1)=vectube(1)-tubecenter(1)
       vectube(2)=vectube(2)-tubecenter(2)
 !C THIS FRAGMENT MAKES TUBE FINITE
 
       vectube(1)=vectube(1)-tubecenter(1)
       vectube(2)=vectube(2)-tubecenter(2)
 !C THIS FRAGMENT MAKES TUBE FINITE
-        positi=(mod(c(3,i+nres),boxzsize))
-        if (positi.le.0) positi=positi+boxzsize
+      positi=(mod(c(3,i+nres),boxzsize))
+      if (positi.le.0) positi=positi+boxzsize
 !C       print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
 !c for each residue check if it is in lipid or lipid water border area
 !C       respos=mod(c(3,i+nres),boxzsize)
 !C       print *,positi,bordtubebot,buftubebot,bordtubetop
 
        if ((positi.gt.bordtubebot)  &
 !C       print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
 !c for each residue check if it is in lipid or lipid water border area
 !C       respos=mod(c(3,i+nres),boxzsize)
 !C       print *,positi,bordtubebot,buftubebot,bordtubetop
 
        if ((positi.gt.bordtubebot)  &
-        .and.(positi.lt.bordtubetop)) then
+      .and.(positi.lt.bordtubetop)) then
 !C the energy transfer exist
 !C the energy transfer exist
-        if (positi.lt.buftubebot) then
-         fracinbuf=1.0d0- &
-            ((positi-bordtubebot)/tubebufthick)
+      if (positi.lt.buftubebot) then
+       fracinbuf=1.0d0- &
+          ((positi-bordtubebot)/tubebufthick)
 !C lipbufthick is thickenes of lipid buffore
 !C lipbufthick is thickenes of lipid buffore
-         sstube=sscalelip(fracinbuf)
-         ssgradtube=-sscagradlip(fracinbuf)/tubebufthick
+       sstube=sscalelip(fracinbuf)
+       ssgradtube=-sscagradlip(fracinbuf)/tubebufthick
 !C         print *,ssgradtube, sstube,tubetranene(itype(i,1))
 !C         print *,ssgradtube, sstube,tubetranene(itype(i,1))
-         enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i,1))
+       enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i,1))
 !C         gg_tube_SC(3,i)=gg_tube_SC(3,i)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C         gg_tube(3,i-1)= gg_tube(3,i-1)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C         print *,"doing sccale for lower part"
 !C         gg_tube_SC(3,i)=gg_tube_SC(3,i)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C         gg_tube(3,i-1)= gg_tube(3,i-1)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C         print *,"doing sccale for lower part"
-        elseif (positi.gt.buftubetop) then
-         fracinbuf=1.0d0- &
-        ((bordtubetop-positi)/tubebufthick)
+      elseif (positi.gt.buftubetop) then
+       fracinbuf=1.0d0- &
+      ((bordtubetop-positi)/tubebufthick)
 
 
-         sstube=sscalelip(fracinbuf)
-         ssgradtube=sscagradlip(fracinbuf)/tubebufthick
-         enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i,1))
+       sstube=sscalelip(fracinbuf)
+       ssgradtube=sscagradlip(fracinbuf)/tubebufthick
+       enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i,1))
 !C         gg_tube_SC(3,i)=gg_tube_SC(3,i)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C         gg_tube(3,i-1)= gg_tube(3,i-1)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C          print *, "doing sscalefor top part",sslip,fracinbuf
 !C         gg_tube_SC(3,i)=gg_tube_SC(3,i)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C         gg_tube(3,i-1)= gg_tube(3,i-1)
 !C     &+ssgradtube*tubetranene(itype(i,1))
 !C          print *, "doing sscalefor top part",sslip,fracinbuf
-        else
-         sstube=1.0d0
-         ssgradtube=0.0d0
-         enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i,1))
+      else
+       sstube=1.0d0
+       ssgradtube=0.0d0
+       enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i,1))
 !C         print *,"I am in true lipid"
 !C         print *,"I am in true lipid"
-        endif
-        else
+      endif
+      else
 !C          sstube=0.0d0
 !C          ssgradtube=0.0d0
 !C          sstube=0.0d0
 !C          ssgradtube=0.0d0
-        cycle
-        endif ! if in lipid or buffor
+      cycle
+      endif ! if in lipid or buffor
 !CEND OF FINITE FRAGMENT
 !C as the tube is infinity we do not calculate the Z-vector use of Z
 !C as chosen axis
 !CEND OF FINITE FRAGMENT
 !C as the tube is infinity we do not calculate the Z-vector use of Z
 !C as chosen axis
@@ -19927,28 +19649,28 @@
        sc_aa_tube=sc_aa_tube_par(iti)
        sc_bb_tube=sc_bb_tube_par(iti)
        enetube(i+nres)=(sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6)&
        sc_aa_tube=sc_aa_tube_par(iti)
        sc_bb_tube=sc_bb_tube_par(iti)
        enetube(i+nres)=(sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6)&
-                       *sstube+enetube(i+nres)
+                   *sstube+enetube(i+nres)
 !C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
 !C now we calculate gradient
        fac=(-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff-&
 !C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
 !C now we calculate gradient
        fac=(-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff-&
-            6.0d0*sc_bb_tube/rdiff6/rdiff)*sstube
+          6.0d0*sc_bb_tube/rdiff6/rdiff)*sstube
 !C now direction of gg_tube vector
 !C now direction of gg_tube vector
-         do j=1,3
-          gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac
-          gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
-         enddo
-         gg_tube_SC(3,i)=gg_tube_SC(3,i) &
+       do j=1,3
+        gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac
+        gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
+       enddo
+       gg_tube_SC(3,i)=gg_tube_SC(3,i) &
        +ssgradtube*enetube(i+nres)/sstube
        +ssgradtube*enetube(i+nres)/sstube
-         gg_tube(3,i-1)= gg_tube(3,i-1) &
+       gg_tube(3,i-1)= gg_tube(3,i-1) &
        +ssgradtube*enetube(i+nres)/sstube
 
        +ssgradtube*enetube(i+nres)/sstube
 
-        enddo
-        do i=itube_start,itube_end
-          Etube=Etube+enetube(i)+enetube(i+nres)
-        enddo
+      enddo
+      do i=itube_start,itube_end
+        Etube=Etube+enetube(i)+enetube(i+nres)
+      enddo
 !C        print *,"ETUBE", etube
 !C        print *,"ETUBE", etube
-        return
-        end subroutine calctube2
+      return
+      end subroutine calctube2
 !=====================================================================================================================================
       subroutine calcnano(Etube)
       real(kind=8),dimension(3) :: vectube
 !=====================================================================================================================================
       subroutine calcnano(Etube)
       real(kind=8),dimension(3) :: vectube
@@ -19961,8 +19683,8 @@
       Etube=0.0d0
 !      print *,itube_start,itube_end,"poczatek"
       do i=itube_start,itube_end
       Etube=0.0d0
 !      print *,itube_start,itube_end,"poczatek"
       do i=itube_start,itube_end
-        enetube(i)=0.0d0
-        enetube(i+nres)=0.0d0
+      enetube(i)=0.0d0
+      enetube(i+nres)=0.0d0
       enddo
 !C first we calculate the distance from tube center
 !C first sugare-phosphate group for NARES this would be peptide group 
       enddo
 !C first we calculate the distance from tube center
 !C first sugare-phosphate group for NARES this would be peptide group 
@@ -19975,32 +19697,32 @@
       ymin=boxysize
       zmin=boxzsize
 
       ymin=boxysize
       zmin=boxzsize
 
-        do j=-1,1
-         vectube(1)=dmod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
-         vectube(1)=vectube(1)+boxxsize*j
-         vectube(2)=dmod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
-         vectube(2)=vectube(2)+boxysize*j
-         vectube(3)=dmod((c(3,i)+c(3,i+1))/2.0d0,boxzsize)
-         vectube(3)=vectube(3)+boxzsize*j
+      do j=-1,1
+       vectube(1)=dmod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+       vectube(1)=vectube(1)+boxxsize*j
+       vectube(2)=dmod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+       vectube(2)=vectube(2)+boxysize*j
+       vectube(3)=dmod((c(3,i)+c(3,i+1))/2.0d0,boxzsize)
+       vectube(3)=vectube(3)+boxzsize*j
 
 
 
 
-         xminact=dabs(vectube(1)-tubecenter(1))
-         yminact=dabs(vectube(2)-tubecenter(2))
-         zminact=dabs(vectube(3)-tubecenter(3))
+       xminact=dabs(vectube(1)-tubecenter(1))
+       yminact=dabs(vectube(2)-tubecenter(2))
+       zminact=dabs(vectube(3)-tubecenter(3))
 
 
-           if (xmin.gt.xminact) then
-            xmin=xminact
-            xtemp=vectube(1)
-           endif
-           if (ymin.gt.yminact) then
-             ymin=yminact
-             ytemp=vectube(2)
-            endif
-           if (zmin.gt.zminact) then
-             zmin=zminact
-             ztemp=vectube(3)
-            endif
-         enddo
+         if (xmin.gt.xminact) then
+          xmin=xminact
+          xtemp=vectube(1)
+         endif
+         if (ymin.gt.yminact) then
+           ymin=yminact
+           ytemp=vectube(2)
+          endif
+         if (zmin.gt.zminact) then
+           zmin=zminact
+           ztemp=vectube(3)
+          endif
+       enddo
       vectube(1)=xtemp
       vectube(2)=ytemp
       vectube(3)=ztemp
       vectube(1)=xtemp
       vectube(2)=ytemp
       vectube(3)=ztemp
@@ -20031,72 +19753,72 @@
 !C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
 !C now we calculate gradient
        fac=(-12.0d0*pep_aa_tube/rdiff6-   &
 !C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
 !C now we calculate gradient
        fac=(-12.0d0*pep_aa_tube/rdiff6-   &
-            6.0d0*pep_bb_tube)/rdiff6/rdiff
+          6.0d0*pep_bb_tube)/rdiff6/rdiff
 !C       write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
 !C     &rdiff,fac
 !C       write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
 !C     &rdiff,fac
-         if (acavtubpep.eq.0.0d0) then
+       if (acavtubpep.eq.0.0d0) then
 !C go to 667
 !C go to 667
-         enecavtube(i)=0.0
-         faccav=0.0
-         else
-         denominator=(1.0d0+dcavtubpep*rdiff6*rdiff6)
-         enecavtube(i)=  &
-        (bcavtubpep*rdiff+acavtubpep*dsqrt(rdiff)+ccavtubpep) &
-        /denominator
-         enecavtube(i)=0.0
-         faccav=((bcavtubpep*1.0d0+acavtubpep/2.0d0/dsqrt(rdiff)) &
-        *denominator-(bcavtubpep*rdiff+acavtubpep*dsqrt(rdiff)   &
-        +ccavtubpep)*rdiff6**2.0d0/rdiff*dcavtubpep*12.0d0)      &
-        /denominator**2.0d0
+       enecavtube(i)=0.0
+       faccav=0.0
+       else
+       denominator=(1.0d0+dcavtubpep*rdiff6*rdiff6)
+       enecavtube(i)=  &
+      (bcavtubpep*rdiff+acavtubpep*dsqrt(rdiff)+ccavtubpep) &
+      /denominator
+       enecavtube(i)=0.0
+       faccav=((bcavtubpep*1.0d0+acavtubpep/2.0d0/dsqrt(rdiff)) &
+      *denominator-(bcavtubpep*rdiff+acavtubpep*dsqrt(rdiff)   &
+      +ccavtubpep)*rdiff6**2.0d0/rdiff*dcavtubpep*12.0d0)      &
+      /denominator**2.0d0
 !C         faccav=0.0
 !C         fac=fac+faccav
 !C 667     continue
 !C         faccav=0.0
 !C         fac=fac+faccav
 !C 667     continue
-         endif
-          if (energy_dec) write(iout,*),i,rdiff,enetube(i),enecavtube(i)
-        do j=1,3
-        gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
-        gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0
-        enddo
-        enddo
+       endif
+        if (energy_dec) write(iout,*),i,rdiff,enetube(i),enecavtube(i)
+      do j=1,3
+      gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
+      gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0
+      enddo
+      enddo
 
        do i=itube_start,itube_end
 
        do i=itube_start,itube_end
-        enecavtube(i)=0.0d0
+      enecavtube(i)=0.0d0
 !C Lets not jump over memory as we use many times iti
 !C Lets not jump over memory as we use many times iti
-         iti=itype(i,1)
+       iti=itype(i,1)
 !C lets ommit dummy atoms for now
 !C lets ommit dummy atoms for now
-         if ((iti.eq.ntyp1) &
+       if ((iti.eq.ntyp1) &
 !C in UNRES uncomment the line below as GLY has no side-chain...
 !C      .or.(iti.eq.10)
 !C in UNRES uncomment the line below as GLY has no side-chain...
 !C      .or.(iti.eq.10)
-         ) cycle
+       ) cycle
       xmin=boxxsize
       ymin=boxysize
       zmin=boxzsize
       xmin=boxxsize
       ymin=boxysize
       zmin=boxzsize
-        do j=-1,1
-         vectube(1)=dmod((c(1,i+nres)),boxxsize)
-         vectube(1)=vectube(1)+boxxsize*j
-         vectube(2)=dmod((c(2,i+nres)),boxysize)
-         vectube(2)=vectube(2)+boxysize*j
-         vectube(3)=dmod((c(3,i+nres)),boxzsize)
-         vectube(3)=vectube(3)+boxzsize*j
-
-
-         xminact=dabs(vectube(1)-tubecenter(1))
-         yminact=dabs(vectube(2)-tubecenter(2))
-         zminact=dabs(vectube(3)-tubecenter(3))
-
-           if (xmin.gt.xminact) then
-            xmin=xminact
-            xtemp=vectube(1)
-           endif
-           if (ymin.gt.yminact) then
-             ymin=yminact
-             ytemp=vectube(2)
-            endif
-           if (zmin.gt.zminact) then
-             zmin=zminact
-             ztemp=vectube(3)
-            endif
-         enddo
+      do j=-1,1
+       vectube(1)=dmod((c(1,i+nres)),boxxsize)
+       vectube(1)=vectube(1)+boxxsize*j
+       vectube(2)=dmod((c(2,i+nres)),boxysize)
+       vectube(2)=vectube(2)+boxysize*j
+       vectube(3)=dmod((c(3,i+nres)),boxzsize)
+       vectube(3)=vectube(3)+boxzsize*j
+
+
+       xminact=dabs(vectube(1)-tubecenter(1))
+       yminact=dabs(vectube(2)-tubecenter(2))
+       zminact=dabs(vectube(3)-tubecenter(3))
+
+         if (xmin.gt.xminact) then
+          xmin=xminact
+          xtemp=vectube(1)
+         endif
+         if (ymin.gt.yminact) then
+           ymin=yminact
+           ytemp=vectube(2)
+          endif
+         if (zmin.gt.zminact) then
+           zmin=zminact
+           ztemp=vectube(3)
+          endif
+       enddo
       vectube(1)=xtemp
       vectube(2)=ytemp
       vectube(3)=ztemp
       vectube(1)=xtemp
       vectube(2)=ytemp
       vectube(3)=ztemp
@@ -20124,46 +19846,46 @@
 !C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
 !C now we calculate gradient
        fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff- &
 !C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
 !C now we calculate gradient
        fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff- &
-            6.0d0*sc_bb_tube/rdiff6/rdiff
+          6.0d0*sc_bb_tube/rdiff6/rdiff
 !C       fac=0.0
 !C now direction of gg_tube vector
 !C Now cavity term E=a(x+bsqrt(x)+c)/(1+dx^12)
 !C       fac=0.0
 !C now direction of gg_tube vector
 !C Now cavity term E=a(x+bsqrt(x)+c)/(1+dx^12)
-         if (acavtub(iti).eq.0.0d0) then
+       if (acavtub(iti).eq.0.0d0) then
 !C go to 667
 !C go to 667
-         enecavtube(i+nres)=0.0d0
-         faccav=0.0d0
-         else
-         denominator=(1.0d0+dcavtub(iti)*rdiff6*rdiff6)
-         enecavtube(i+nres)=   &
-        (bcavtub(iti)*rdiff+acavtub(iti)*dsqrt(rdiff)+ccavtub(iti)) &
-        /denominator
+       enecavtube(i+nres)=0.0d0
+       faccav=0.0d0
+       else
+       denominator=(1.0d0+dcavtub(iti)*rdiff6*rdiff6)
+       enecavtube(i+nres)=   &
+      (bcavtub(iti)*rdiff+acavtub(iti)*dsqrt(rdiff)+ccavtub(iti)) &
+      /denominator
 !C         enecavtube(i)=0.0
 !C         enecavtube(i)=0.0
-         faccav=((bcavtub(iti)*1.0d0+acavtub(iti)/2.0d0/dsqrt(rdiff)) &
-        *denominator-(bcavtub(iti)*rdiff+acavtub(iti)*dsqrt(rdiff)   &
-        +ccavtub(iti))*rdiff6**2.0d0/rdiff*dcavtub(iti)*12.0d0)      &
-        /denominator**2.0d0
+       faccav=((bcavtub(iti)*1.0d0+acavtub(iti)/2.0d0/dsqrt(rdiff)) &
+      *denominator-(bcavtub(iti)*rdiff+acavtub(iti)*dsqrt(rdiff)   &
+      +ccavtub(iti))*rdiff6**2.0d0/rdiff*dcavtub(iti)*12.0d0)      &
+      /denominator**2.0d0
 !C         faccav=0.0
 !C         faccav=0.0
-         fac=fac+faccav
+       fac=fac+faccav
 !C 667     continue
 !C 667     continue
-         endif
+       endif
 !C         print *,"TUT",i,iti,rdiff,rdiff6,acavtub(iti),denominator,
 !C     &   enecavtube(i),faccav
 !C         print *,"licz=",
 !C     & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti))
 !C         print *,"finene=",enetube(i+nres)+enecavtube(i)
 !C         print *,"TUT",i,iti,rdiff,rdiff6,acavtub(iti),denominator,
 !C     &   enecavtube(i),faccav
 !C         print *,"licz=",
 !C     & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti))
 !C         print *,"finene=",enetube(i+nres)+enecavtube(i)
-         do j=1,3
-          gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac
-          gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
-         enddo
-          if (energy_dec) write(iout,*),i,rdiff,enetube(i+nres),enecavtube(i+nres)
-        enddo
+       do j=1,3
+        gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac
+        gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
+       enddo
+        if (energy_dec) write(iout,*),i,rdiff,enetube(i+nres),enecavtube(i+nres)
+      enddo
 
 
 
 
 
 
-        do i=itube_start,itube_end
-          Etube=Etube+enetube(i)+enetube(i+nres)+enecavtube(i) &
-         +enecavtube(i+nres)
-        enddo
+      do i=itube_start,itube_end
+        Etube=Etube+enetube(i)+enetube(i+nres)+enecavtube(i) &
+       +enecavtube(i+nres)
+      enddo
 !        do i=1,20
 !         print *,"begin", i,"a"
 !         do r=1,10000
 !        do i=1,20
 !         print *,"begin", i,"a"
 !         do r=1,10000
@@ -20182,8 +19904,8 @@
 !         print *,"end",i,"a"
 !        enddo
 !C        print *,"ETUBE", etube
 !         print *,"end",i,"a"
 !        enddo
 !C        print *,"ETUBE", etube
-        return
-        end subroutine calcnano
+      return
+      end subroutine calcnano
 
 !===============================================
 !--------------------------------------------------------------------------------
 
 !===============================================
 !--------------------------------------------------------------------------------
@@ -20191,24 +19913,24 @@
 
        subroutine set_shield_fac2
        real(kind=8) :: div77_81=0.974996043d0, &
 
        subroutine set_shield_fac2
        real(kind=8) :: div77_81=0.974996043d0, &
-        div4_81=0.2222222222d0
+      div4_81=0.2222222222d0
        real (kind=8) :: dist_pep_side,dist_side_calf,dist_pept_group, &
        real (kind=8) :: dist_pep_side,dist_side_calf,dist_pept_group, &
-         scale_fac_dist,fac_help_scale,VofOverlap,VolumeTotal,costhet,&
-         short,long,sinthet,costhet_fac,sh_frac_dist,rkprim,cosphi,   &
-         sinphi,cosphi_fac,pep_side0pept_group,cosalfa,fac_alfa_sin
+       scale_fac_dist,fac_help_scale,VofOverlap,VolumeTotal,costhet,&
+       short,long,sinthet,costhet_fac,sh_frac_dist,rkprim,cosphi,   &
+       sinphi,cosphi_fac,pep_side0pept_group,cosalfa,fac_alfa_sin
 !C the vector between center of side_chain and peptide group
        real(kind=8),dimension(3) :: pep_side_long,side_calf, &
 !C the vector between center of side_chain and peptide group
        real(kind=8),dimension(3) :: pep_side_long,side_calf, &
-         pept_group,costhet_grad,cosphi_grad_long, &
-         cosphi_grad_loc,pep_side_norm,side_calf_norm, &
-         sh_frac_dist_grad,pep_side
-        integer i,j,k
+       pept_group,costhet_grad,cosphi_grad_long, &
+       cosphi_grad_loc,pep_side_norm,side_calf_norm, &
+       sh_frac_dist_grad,pep_side
+      integer i,j,k
 !C      write(2,*) "ivec",ivec_start,ivec_end
       do i=1,nres
 !C      write(2,*) "ivec",ivec_start,ivec_end
       do i=1,nres
-        fac_shield(i)=0.0d0
-        ishield_list(i)=0
-        do j=1,3
-        grad_shield(j,i)=0.0d0
-        enddo
+      fac_shield(i)=0.0d0
+      ishield_list(i)=0
+      do j=1,3
+      grad_shield(j,i)=0.0d0
+      enddo
       enddo
       do i=ivec_start,ivec_end
 !C      do i=1,nres-1
       enddo
       do i=ivec_start,ivec_end
 !C      do i=1,nres-1
@@ -20239,40 +19961,40 @@
        dist_pept_group=sqrt(dist_pept_group)
        dist_side_calf=sqrt(dist_side_calf)
       do j=1,3
        dist_pept_group=sqrt(dist_pept_group)
        dist_side_calf=sqrt(dist_side_calf)
       do j=1,3
-        pep_side_norm(j)=pep_side(j)/dist_pep_side
-        side_calf_norm(j)=dist_side_calf
+      pep_side_norm(j)=pep_side(j)/dist_pep_side
+      side_calf_norm(j)=dist_side_calf
       enddo
 !C now sscale fraction
        sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield
 !       print *,buff_shield,"buff",sh_frac_dist
 !C now sscale
       enddo
 !C now sscale fraction
        sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield
 !       print *,buff_shield,"buff",sh_frac_dist
 !C now sscale
-        if (sh_frac_dist.le.0.0) cycle
+      if (sh_frac_dist.le.0.0) cycle
 !C        print *,ishield_list(i),i
 !C If we reach here it means that this side chain reaches the shielding sphere
 !C Lets add him to the list for gradient       
 !C        print *,ishield_list(i),i
 !C If we reach here it means that this side chain reaches the shielding sphere
 !C Lets add him to the list for gradient       
-        ishield_list(i)=ishield_list(i)+1
+      ishield_list(i)=ishield_list(i)+1
 !C ishield_list is a list of non 0 side-chain that contribute to factor gradient
 !C this list is essential otherwise problem would be O3
 !C ishield_list is a list of non 0 side-chain that contribute to factor gradient
 !C this list is essential otherwise problem would be O3
-        shield_list(ishield_list(i),i)=k
+      shield_list(ishield_list(i),i)=k
 !C Lets have the sscale value
 !C Lets have the sscale value
-        if (sh_frac_dist.gt.1.0) then
-         scale_fac_dist=1.0d0
-         do j=1,3
-         sh_frac_dist_grad(j)=0.0d0
-         enddo
-        else
-         scale_fac_dist=-sh_frac_dist*sh_frac_dist &
-                        *(2.0d0*sh_frac_dist-3.0d0)
-         fac_help_scale=6.0d0*(sh_frac_dist-sh_frac_dist**2) &
-                       /dist_pep_side/buff_shield*0.5d0
-         do j=1,3
-         sh_frac_dist_grad(j)=fac_help_scale*pep_side(j)
+      if (sh_frac_dist.gt.1.0) then
+       scale_fac_dist=1.0d0
+       do j=1,3
+       sh_frac_dist_grad(j)=0.0d0
+       enddo
+      else
+       scale_fac_dist=-sh_frac_dist*sh_frac_dist &
+                  *(2.0d0*sh_frac_dist-3.0d0)
+       fac_help_scale=6.0d0*(sh_frac_dist-sh_frac_dist**2) &
+                   /dist_pep_side/buff_shield*0.5d0
+       do j=1,3
+       sh_frac_dist_grad(j)=fac_help_scale*pep_side(j)
 !C         sh_frac_dist_grad(j)=0.0d0
 !C         scale_fac_dist=1.0d0
 !C         print *,"jestem",scale_fac_dist,fac_help_scale,
 !C     &                    sh_frac_dist_grad(j)
 !C         sh_frac_dist_grad(j)=0.0d0
 !C         scale_fac_dist=1.0d0
 !C         print *,"jestem",scale_fac_dist,fac_help_scale,
 !C     &                    sh_frac_dist_grad(j)
-         enddo
-        endif
+       enddo
+      endif
 !C this is what is now we have the distance scaling now volume...
       short=short_r_sidechain(itype(k,1))
       long=long_r_sidechain(itype(k,1))
 !C this is what is now we have the distance scaling now volume...
       short=short_r_sidechain(itype(k,1))
       long=long_r_sidechain(itype(k,1))
@@ -20287,7 +20009,7 @@
 !C     &             -short/dist_pep_side**2/costhet)
 !C       costhet_fac=0.0d0
        do j=1,3
 !C     &             -short/dist_pep_side**2/costhet)
 !C       costhet_fac=0.0d0
        do j=1,3
-         costhet_grad(j)=costhet_fac*pep_side(j)
+       costhet_grad(j)=costhet_fac*pep_side(j)
        enddo
 !C remember for the final gradient multiply costhet_grad(j) 
 !C for side_chain by factor -2 !
        enddo
 !C remember for the final gradient multiply costhet_grad(j) 
 !C for side_chain by factor -2 !
@@ -20309,17 +20031,17 @@
 !C       cosphi=0.6
        cosphi_fac=cosphi**3*rkprim**2*(-0.5d0)/dist_pep_side**4
        sinphi=rkprim/dist_pep_side/dsqrt(1.0d0+rkprim**2/ &
 !C       cosphi=0.6
        cosphi_fac=cosphi**3*rkprim**2*(-0.5d0)/dist_pep_side**4
        sinphi=rkprim/dist_pep_side/dsqrt(1.0d0+rkprim**2/ &
-           dist_pep_side**2)
+         dist_pep_side**2)
 !C       sinphi=0.8
        do j=1,3
 !C       sinphi=0.8
        do j=1,3
-         cosphi_grad_long(j)=cosphi_fac*pep_side(j) &
+       cosphi_grad_long(j)=cosphi_fac*pep_side(j) &
       +cosphi**3*0.5d0/dist_pep_side**2*(-rkprim) &
       *(long-short)/fac_alfa_sin*cosalfa/ &
       ((dist_pep_side*dist_side_calf))* &
       ((side_calf(j))-cosalfa* &
       ((pep_side(j)/dist_pep_side)*dist_side_calf))
 !C       cosphi_grad_long(j)=0.0d0
       +cosphi**3*0.5d0/dist_pep_side**2*(-rkprim) &
       *(long-short)/fac_alfa_sin*cosalfa/ &
       ((dist_pep_side*dist_side_calf))* &
       ((side_calf(j))-cosalfa* &
       ((pep_side(j)/dist_pep_side)*dist_side_calf))
 !C       cosphi_grad_long(j)=0.0d0
-        cosphi_grad_loc(j)=cosphi**3*0.5d0/dist_pep_side**2*(-rkprim) &
+      cosphi_grad_loc(j)=cosphi**3*0.5d0/dist_pep_side**2*(-rkprim) &
       *(long-short)/fac_alfa_sin*cosalfa &
       /((dist_pep_side*dist_side_calf))* &
       (pep_side(j)- &
       *(long-short)/fac_alfa_sin*cosalfa &
       /((dist_pep_side*dist_side_calf))* &
       (pep_side(j)- &
@@ -20328,37 +20050,37 @@
        enddo
 !C      print *,sinphi,sinthet
       VofOverlap=VSolvSphere/2.0d0*(1.0d0-dsqrt(1.0d0-sinphi*sinthet)) &
        enddo
 !C      print *,sinphi,sinthet
       VofOverlap=VSolvSphere/2.0d0*(1.0d0-dsqrt(1.0d0-sinphi*sinthet)) &
-                         /VSolvSphere_div
+                   /VSolvSphere_div
 !C     &                    *wshield
 !C now the gradient...
       do j=1,3
       grad_shield(j,i)=grad_shield(j,i) &
 !C gradient po skalowaniu
 !C     &                    *wshield
 !C now the gradient...
       do j=1,3
       grad_shield(j,i)=grad_shield(j,i) &
 !C gradient po skalowaniu
-                     +(sh_frac_dist_grad(j)*VofOverlap &
+                 +(sh_frac_dist_grad(j)*VofOverlap &
 !C  gradient po costhet
 !C  gradient po costhet
-            +scale_fac_dist*VSolvSphere/VSolvSphere_div/4.0d0* &
-        (1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*( &
-            sinphi/sinthet*costhet*costhet_grad(j) &
-           +sinthet/sinphi*cosphi*cosphi_grad_long(j))) &
-        )*wshield
+          +scale_fac_dist*VSolvSphere/VSolvSphere_div/4.0d0* &
+      (1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*( &
+          sinphi/sinthet*costhet*costhet_grad(j) &
+         +sinthet/sinphi*cosphi*cosphi_grad_long(j))) &
+      )*wshield
 !C grad_shield_side is Cbeta sidechain gradient
       grad_shield_side(j,ishield_list(i),i)=&
 !C grad_shield_side is Cbeta sidechain gradient
       grad_shield_side(j,ishield_list(i),i)=&
-             (sh_frac_dist_grad(j)*-2.0d0&
-             *VofOverlap&
-            -scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0*&
+           (sh_frac_dist_grad(j)*-2.0d0&
+           *VofOverlap&
+          -scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0*&
        (1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*(&
        (1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*(&
-            sinphi/sinthet*costhet*costhet_grad(j)&
-           +sinthet/sinphi*cosphi*cosphi_grad_long(j))) &
-            )*wshield
+          sinphi/sinthet*costhet*costhet_grad(j)&
+         +sinthet/sinphi*cosphi*cosphi_grad_long(j))) &
+          )*wshield
 !       print *, 1.0d0/(-dsqrt(1.0d0-sinphi*sinthet)),&
 !            sinphi/sinthet,&
 !           +sinthet/sinphi,"HERE"
        grad_shield_loc(j,ishield_list(i),i)=   &
 !       print *, 1.0d0/(-dsqrt(1.0d0-sinphi*sinthet)),&
 !            sinphi/sinthet,&
 !           +sinthet/sinphi,"HERE"
        grad_shield_loc(j,ishield_list(i),i)=   &
-            scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0*&
+          scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0*&
       (1.0d0/(dsqrt(1.0d0-sinphi*sinthet))*(&
       (1.0d0/(dsqrt(1.0d0-sinphi*sinthet))*(&
-            sinthet/sinphi*cosphi*cosphi_grad_loc(j)&
-             ))&
-             *wshield
+          sinthet/sinphi*cosphi*cosphi_grad_loc(j)&
+           ))&
+           *wshield
 !         print *,grad_shield_loc(j,ishield_list(i),i)
       enddo
       VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist
 !         print *,grad_shield_loc(j,ishield_list(i),i)
       enddo
       VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist
@@ -20439,9 +20161,9 @@
       character(len=80) :: controlcard
 
       do i=1,dyn_nssHist
       character(len=80) :: controlcard
 
       do i=1,dyn_nssHist
-        call card_concat(controlcard,.true.)
-        read(controlcard,*) &
-             dyn_ssHist(i,0),(dyn_ssHist(i,j),j=1,2*dyn_ssHist(i,0))
+      call card_concat(controlcard,.true.)
+      read(controlcard,*) &
+           dyn_ssHist(i,0),(dyn_ssHist(i,j),j=1,2*dyn_ssHist(i,0))
       enddo
 
       return
       enddo
 
       return
@@ -20452,16 +20174,16 @@
 !el
 ! get the position of the jth ijth fragment of the chain coordinate system      
 ! in the fromto array.
 !el
 ! get the position of the jth ijth fragment of the chain coordinate system      
 ! in the fromto array.
-        integer :: i,j
+      integer :: i,j
 
 
-        indmat=((2*(nres-2)-i)*(i-1))/2+j-1
+      indmat=((2*(nres-2)-i)*(i-1))/2+j-1
       return
       end function indmat
 !-----------------------------------------------------------------------------
       real(kind=8) function sigm(x)
 !el   
        real(kind=8) :: x
       return
       end function indmat
 !-----------------------------------------------------------------------------
       real(kind=8) function sigm(x)
 !el   
        real(kind=8) :: x
-        sigm=0.25d0*x
+      sigm=0.25d0*x
       return
       end function sigm
 !-----------------------------------------------------------------------------
       return
       end function sigm
 !-----------------------------------------------------------------------------
@@ -20473,11 +20195,11 @@
       integer :: i,j
       
       if(nres.lt.100) then
       integer :: i,j
       
       if(nres.lt.100) then
-        maxconts=nres
+      maxconts=10*nres
       elseif(nres.lt.200) then
       elseif(nres.lt.200) then
-        maxconts=0.8*nres      ! Max. number of contacts per residue
+      maxconts=10*nres      ! Max. number of contacts per residue
       else
       else
-        maxconts=0.6*nres ! (maxconts=maxres/4)
+      maxconts=10*nres ! (maxconts=maxres/4)
       endif
       maxcont=12*nres      ! Max. number of SC contacts
       maxvar=6*nres      ! Max. number of variables
       endif
       maxcont=12*nres      ! Max. number of SC contacts
       maxvar=6*nres      ! Max. number of variables
@@ -20723,6 +20445,8 @@
       allocate(gradpepcat(3,-1:nres))
       allocate(gradpepcatx(3,-1:nres))
       allocate(gradcatcat(3,-1:nres))
       allocate(gradpepcat(3,-1:nres))
       allocate(gradpepcatx(3,-1:nres))
       allocate(gradcatcat(3,-1:nres))
+      allocate(gradnuclcat(3,-1:nres))
+      allocate(gradnuclcatx(3,-1:nres))
 !(3,maxres)
       allocate(grad_shield_side(3,maxcontsshi,-1:nres))
       allocate(grad_shield_loc(3,maxcontsshi,-1:nres))
 !(3,maxres)
       allocate(grad_shield_side(3,maxcontsshi,-1:nres))
       allocate(grad_shield_loc(3,maxcontsshi,-1:nres))
@@ -20851,7 +20575,7 @@
 !      enddo
 
 !      if (nss.gt.0) then
 !      enddo
 
 !      if (nss.gt.0) then
-        allocate(idssb(maxdim),jdssb(maxdim))
+      allocate(idssb(maxdim),jdssb(maxdim))
 !        allocate(newihpb(nss),newjhpb(nss))
 !(maxdim)
 !      endif
 !        allocate(newihpb(nss),newjhpb(nss))
 !(maxdim)
 !      endif
@@ -20905,6 +20629,13 @@
       allocate(uygrad(3,3,2,nres))
       allocate(uzgrad(3,3,2,nres))
 !(3,3,2,maxres)
       allocate(uygrad(3,3,2,nres))
       allocate(uzgrad(3,3,2,nres))
 !(3,3,2,maxres)
+! allocateion of lists JPRDLA
+      allocate(newcontlistppi(300*nres))
+      allocate(newcontlistscpi(350*nres))
+      allocate(newcontlisti(300*nres))
+      allocate(newcontlistppj(300*nres))
+      allocate(newcontlistscpj(350*nres))
+      allocate(newcontlistj(300*nres))
 
       return
       end subroutine alloc_ener_arrays
 
       return
       end subroutine alloc_ener_arrays
@@ -20924,8 +20655,8 @@
       write (iout,*) "ibondp_start,ibondp_end",&
        ibondp_nucl_start,ibondp_nucl_end
       do i=ibondp_nucl_start,ibondp_nucl_end
       write (iout,*) "ibondp_start,ibondp_end",&
        ibondp_nucl_start,ibondp_nucl_end
       do i=ibondp_nucl_start,ibondp_nucl_end
-        if (itype(i-1,2).eq.ntyp1_molec(2) .or. &
-         itype(i,2).eq.ntyp1_molec(2)) cycle
+      if (itype(i-1,2).eq.ntyp1_molec(2) .or. &
+       itype(i,2).eq.ntyp1_molec(2)) cycle
 !          estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax)
 !          do j=1,3
 !          gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax)
 !          estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax)
 !          do j=1,3
 !          gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax)
@@ -20935,14 +20666,14 @@
 !     &       "estr1",i,vbld(i),distchainmax,
 !     &       gnmr1(vbld(i),-1.0d0,distchainmax)
 
 !     &       "estr1",i,vbld(i),distchainmax,
 !     &       gnmr1(vbld(i),-1.0d0,distchainmax)
 
-          diff = vbld(i)-vbldp0_nucl
-          if(energy_dec)write(iout,*) "estr_nucl_bb" , i,vbld(i),&
-          vbldp0_nucl,diff,AKP_nucl*diff*diff
-          estr_nucl=estr_nucl+diff*diff
+        diff = vbld(i)-vbldp0_nucl
+        if(energy_dec)write(iout,*) "estr_nucl_bb" , i,vbld(i),&
+        vbldp0_nucl,diff,AKP_nucl*diff*diff
+        estr_nucl=estr_nucl+diff*diff
 !          print *,estr_nucl
 !          print *,estr_nucl
-          do j=1,3
-            gradb_nucl(j,i-1)=AKP_nucl*diff*dc(j,i-1)/vbld(i)
-          enddo
+        do j=1,3
+          gradb_nucl(j,i-1)=AKP_nucl*diff*dc(j,i-1)/vbld(i)
+        enddo
 !c          write (iout,'(i5,3f10.5)') i,(gradb(j,i-1),j=1,3)
       enddo
       estr_nucl=0.5d0*AKP_nucl*estr_nucl
 !c          write (iout,'(i5,3f10.5)') i,(gradb(j,i-1),j=1,3)
       enddo
       estr_nucl=0.5d0*AKP_nucl*estr_nucl
@@ -20954,50 +20685,50 @@
 
       do i=ibond_nucl_start,ibond_nucl_end
 !C        print *, "I am stuck",i
 
       do i=ibond_nucl_start,ibond_nucl_end
 !C        print *, "I am stuck",i
-        iti=itype(i,2)
-        if (iti.eq.ntyp1_molec(2)) cycle
-          nbi=nbondterm_nucl(iti)
+      iti=itype(i,2)
+      if (iti.eq.ntyp1_molec(2)) cycle
+        nbi=nbondterm_nucl(iti)
 !C        print *,iti,nbi
 !C        print *,iti,nbi
-          if (nbi.eq.1) then
-            diff=vbld(i+nres)-vbldsc0_nucl(1,iti)
+        if (nbi.eq.1) then
+          diff=vbld(i+nres)-vbldsc0_nucl(1,iti)
 
 
-            if (energy_dec) &
-           write (iout,*) "estr_nucl_sc", i,iti,vbld(i+nres),vbldsc0_nucl(1,iti),diff, &
-           AKSC_nucl(1,iti),AKSC_nucl(1,iti)*diff*diff
-            estr_nucl=estr_nucl+0.5d0*AKSC_nucl(1,iti)*diff*diff
+          if (energy_dec) &
+         write (iout,*) "estr_nucl_sc", i,iti,vbld(i+nres),vbldsc0_nucl(1,iti),diff, &
+         AKSC_nucl(1,iti),AKSC_nucl(1,iti)*diff*diff
+          estr_nucl=estr_nucl+0.5d0*AKSC_nucl(1,iti)*diff*diff
 !            print *,estr_nucl
 !            print *,estr_nucl
-            do j=1,3
-              gradbx_nucl(j,i)=AKSC_nucl(1,iti)*diff*dc(j,i+nres)/vbld(i+nres)
-            enddo
-          else
-            do j=1,nbi
-              diff=vbld(i+nres)-vbldsc0_nucl(j,iti)
-              ud(j)=aksc_nucl(j,iti)*diff
-              u(j)=abond0_nucl(j,iti)+0.5d0*ud(j)*diff
-            enddo
-            uprod=u(1)
-            do j=2,nbi
-              uprod=uprod*u(j)
-            enddo
-            usum=0.0d0
-            usumsqder=0.0d0
-            do j=1,nbi
-              uprod1=1.0d0
-              uprod2=1.0d0
-              do k=1,nbi
-                if (k.ne.j) then
-                  uprod1=uprod1*u(k)
-                  uprod2=uprod2*u(k)*u(k)
-                endif
-              enddo
-              usum=usum+uprod1
-              usumsqder=usumsqder+ud(j)*uprod2
-            enddo
-            estr_nucl=estr_nucl+uprod/usum
-            do j=1,3
-             gradbx_nucl(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres)
+          do j=1,3
+            gradbx_nucl(j,i)=AKSC_nucl(1,iti)*diff*dc(j,i+nres)/vbld(i+nres)
+          enddo
+        else
+          do j=1,nbi
+            diff=vbld(i+nres)-vbldsc0_nucl(j,iti)
+            ud(j)=aksc_nucl(j,iti)*diff
+            u(j)=abond0_nucl(j,iti)+0.5d0*ud(j)*diff
+          enddo
+          uprod=u(1)
+          do j=2,nbi
+            uprod=uprod*u(j)
+          enddo
+          usum=0.0d0
+          usumsqder=0.0d0
+          do j=1,nbi
+            uprod1=1.0d0
+            uprod2=1.0d0
+            do k=1,nbi
+            if (k.ne.j) then
+              uprod1=uprod1*u(k)
+              uprod2=uprod2*u(k)*u(k)
+            endif
             enddo
             enddo
-        endif
+            usum=usum+uprod1
+            usumsqder=usumsqder+ud(j)*uprod2
+          enddo
+          estr_nucl=estr_nucl+uprod/usum
+          do j=1,3
+           gradbx_nucl(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres)
+          enddo
+      endif
       enddo
 !C      print *,"I am about to leave ebond"
       return
       enddo
 !C      print *,"I am about to leave ebond"
       return
@@ -21019,168 +20750,168 @@
       etheta_nucl=0.0D0
 !      print *,"ithet_start",ithet_nucl_start," ithet_end",ithet_nucl_end,nres
       do i=ithet_nucl_start,ithet_nucl_end
       etheta_nucl=0.0D0
 !      print *,"ithet_start",ithet_nucl_start," ithet_end",ithet_nucl_end,nres
       do i=ithet_nucl_start,ithet_nucl_end
-        if ((itype(i-1,2).eq.ntyp1_molec(2)).or.&
-        (itype(i-2,2).eq.ntyp1_molec(2)).or.     &
-        (itype(i,2).eq.ntyp1_molec(2))) cycle
-        dethetai=0.0d0
-        dephii=0.0d0
-        dephii1=0.0d0
-        theti2=0.5d0*theta(i)
-        ityp2=ithetyp_nucl(itype(i-1,2))
-        do k=1,nntheterm_nucl
-          coskt(k)=dcos(k*theti2)
-          sinkt(k)=dsin(k*theti2)
-        enddo
-        if (i.gt.3 .and. itype(i-2,2).ne.ntyp1_molec(2)) then
+      if ((itype(i-1,2).eq.ntyp1_molec(2)).or.&
+      (itype(i-2,2).eq.ntyp1_molec(2)).or.     &
+      (itype(i,2).eq.ntyp1_molec(2))) cycle
+      dethetai=0.0d0
+      dephii=0.0d0
+      dephii1=0.0d0
+      theti2=0.5d0*theta(i)
+      ityp2=ithetyp_nucl(itype(i-1,2))
+      do k=1,nntheterm_nucl
+        coskt(k)=dcos(k*theti2)
+        sinkt(k)=dsin(k*theti2)
+      enddo
+      if (i.gt.3 .and. itype(i-2,2).ne.ntyp1_molec(2)) then
 #ifdef OSF
 #ifdef OSF
-          phii=phi(i)
-          if (phii.ne.phii) phii=150.0
+        phii=phi(i)
+        if (phii.ne.phii) phii=150.0
 #else
 #else
-          phii=phi(i)
+        phii=phi(i)
 #endif
 #endif
-          ityp1=ithetyp_nucl(itype(i-2,2))
-          do k=1,nsingle_nucl
-            cosph1(k)=dcos(k*phii)
-            sinph1(k)=dsin(k*phii)
-          enddo
-        else
-          phii=0.0d0
-          ityp1=nthetyp_nucl+1
-          do k=1,nsingle_nucl
-            cosph1(k)=0.0d0
-            sinph1(k)=0.0d0
-          enddo
-        endif
+        ityp1=ithetyp_nucl(itype(i-2,2))
+        do k=1,nsingle_nucl
+          cosph1(k)=dcos(k*phii)
+          sinph1(k)=dsin(k*phii)
+        enddo
+      else
+        phii=0.0d0
+        ityp1=nthetyp_nucl+1
+        do k=1,nsingle_nucl
+          cosph1(k)=0.0d0
+          sinph1(k)=0.0d0
+        enddo
+      endif
 
 
-        if (i.lt.nres .and. itype(i,2).ne.ntyp1_molec(2)) then
+      if (i.lt.nres .and. itype(i,2).ne.ntyp1_molec(2)) then
 #ifdef OSF
 #ifdef OSF
-          phii1=phi(i+1)
-          if (phii1.ne.phii1) phii1=150.0
-          phii1=pinorm(phii1)
+        phii1=phi(i+1)
+        if (phii1.ne.phii1) phii1=150.0
+        phii1=pinorm(phii1)
 #else
 #else
-          phii1=phi(i+1)
+        phii1=phi(i+1)
 #endif
 #endif
-          ityp3=ithetyp_nucl(itype(i,2))
-          do k=1,nsingle_nucl
-            cosph2(k)=dcos(k*phii1)
-            sinph2(k)=dsin(k*phii1)
-          enddo
-        else
-          phii1=0.0d0
-          ityp3=nthetyp_nucl+1
-          do k=1,nsingle_nucl
-            cosph2(k)=0.0d0
-            sinph2(k)=0.0d0
-          enddo
-        endif
-        ethetai=aa0thet_nucl(ityp1,ityp2,ityp3)
-        do k=1,ndouble_nucl
-          do l=1,k-1
-            ccl=cosph1(l)*cosph2(k-l)
-            ssl=sinph1(l)*sinph2(k-l)
-            scl=sinph1(l)*cosph2(k-l)
-            csl=cosph1(l)*sinph2(k-l)
-            cosph1ph2(l,k)=ccl-ssl
-            cosph1ph2(k,l)=ccl+ssl
-            sinph1ph2(l,k)=scl+csl
-            sinph1ph2(k,l)=scl-csl
-          enddo
+        ityp3=ithetyp_nucl(itype(i,2))
+        do k=1,nsingle_nucl
+          cosph2(k)=dcos(k*phii1)
+          sinph2(k)=dsin(k*phii1)
         enddo
         enddo
-        if (lprn) then
-        write (iout,*) "i",i," ityp1",ityp1," ityp2",ityp2,&
-         " ityp3",ityp3," theti2",theti2," phii",phii," phii1",phii1
-        write (iout,*) "coskt and sinkt",nntheterm_nucl
-        do k=1,nntheterm_nucl
-          write (iout,*) k,coskt(k),sinkt(k)
+      else
+        phii1=0.0d0
+        ityp3=nthetyp_nucl+1
+        do k=1,nsingle_nucl
+          cosph2(k)=0.0d0
+          sinph2(k)=0.0d0
         enddo
         enddo
-        endif
-        do k=1,ntheterm_nucl
-          ethetai=ethetai+aathet_nucl(k,ityp1,ityp2,ityp3)*sinkt(k)
-          dethetai=dethetai+0.5d0*k*aathet_nucl(k,ityp1,ityp2,ityp3)&
-           *coskt(k)
-          if (lprn)&
-         write (iout,*) "k",k," aathet",aathet_nucl(k,ityp1,ityp2,ityp3),&
-          " ethetai",ethetai
+      endif
+      ethetai=aa0thet_nucl(ityp1,ityp2,ityp3)
+      do k=1,ndouble_nucl
+        do l=1,k-1
+          ccl=cosph1(l)*cosph2(k-l)
+          ssl=sinph1(l)*sinph2(k-l)
+          scl=sinph1(l)*cosph2(k-l)
+          csl=cosph1(l)*sinph2(k-l)
+          cosph1ph2(l,k)=ccl-ssl
+          cosph1ph2(k,l)=ccl+ssl
+          sinph1ph2(l,k)=scl+csl
+          sinph1ph2(k,l)=scl-csl
         enddo
         enddo
-        if (lprn) then
-        write (iout,*) "cosph and sinph"
+      enddo
+      if (lprn) then
+      write (iout,*) "i",i," ityp1",ityp1," ityp2",ityp2,&
+       " ityp3",ityp3," theti2",theti2," phii",phii," phii1",phii1
+      write (iout,*) "coskt and sinkt",nntheterm_nucl
+      do k=1,nntheterm_nucl
+        write (iout,*) k,coskt(k),sinkt(k)
+      enddo
+      endif
+      do k=1,ntheterm_nucl
+        ethetai=ethetai+aathet_nucl(k,ityp1,ityp2,ityp3)*sinkt(k)
+        dethetai=dethetai+0.5d0*k*aathet_nucl(k,ityp1,ityp2,ityp3)&
+         *coskt(k)
+        if (lprn)&
+       write (iout,*) "k",k," aathet",aathet_nucl(k,ityp1,ityp2,ityp3),&
+        " ethetai",ethetai
+      enddo
+      if (lprn) then
+      write (iout,*) "cosph and sinph"
+      do k=1,nsingle_nucl
+        write (iout,*) k,cosph1(k),sinph1(k),cosph2(k),sinph2(k)
+      enddo
+      write (iout,*) "cosph1ph2 and sinph2ph2"
+      do k=2,ndouble_nucl
+        do l=1,k-1
+          write (iout,*) l,k,cosph1ph2(l,k),cosph1ph2(k,l),&
+            sinph1ph2(l,k),sinph1ph2(k,l)
+        enddo
+      enddo
+      write(iout,*) "ethetai",ethetai
+      endif
+      do m=1,ntheterm2_nucl
         do k=1,nsingle_nucl
         do k=1,nsingle_nucl
-          write (iout,*) k,cosph1(k),sinph1(k),cosph2(k),sinph2(k)
+          aux=bbthet_nucl(k,m,ityp1,ityp2,ityp3)*cosph1(k)&
+            +ccthet_nucl(k,m,ityp1,ityp2,ityp3)*sinph1(k)&
+            +ddthet_nucl(k,m,ityp1,ityp2,ityp3)*cosph2(k)&
+            +eethet_nucl(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+          ethetai=ethetai+sinkt(m)*aux
+          dethetai=dethetai+0.5d0*m*aux*coskt(m)
+          dephii=dephii+k*sinkt(m)*(&
+             ccthet_nucl(k,m,ityp1,ityp2,ityp3)*cosph1(k)-&
+             bbthet_nucl(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+          dephii1=dephii1+k*sinkt(m)*(&
+             eethet_nucl(k,m,ityp1,ityp2,ityp3)*cosph2(k)-&
+             ddthet_nucl(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+          if (lprn) &
+         write (iout,*) "m",m," k",k," bbthet",&
+            bbthet_nucl(k,m,ityp1,ityp2,ityp3)," ccthet",&
+            ccthet_nucl(k,m,ityp1,ityp2,ityp3)," ddthet",&
+            ddthet_nucl(k,m,ityp1,ityp2,ityp3)," eethet",&
+            eethet_nucl(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
         enddo
         enddo
-        write (iout,*) "cosph1ph2 and sinph2ph2"
+      enddo
+      if (lprn) &
+      write(iout,*) "ethetai",ethetai
+      do m=1,ntheterm3_nucl
         do k=2,ndouble_nucl
           do l=1,k-1
         do k=2,ndouble_nucl
           do l=1,k-1
-            write (iout,*) l,k,cosph1ph2(l,k),cosph1ph2(k,l),&
-              sinph1ph2(l,k),sinph1ph2(k,l)
-          enddo
-        enddo
-        write(iout,*) "ethetai",ethetai
-        endif
-        do m=1,ntheterm2_nucl
-          do k=1,nsingle_nucl
-            aux=bbthet_nucl(k,m,ityp1,ityp2,ityp3)*cosph1(k)&
-              +ccthet_nucl(k,m,ityp1,ityp2,ityp3)*sinph1(k)&
-              +ddthet_nucl(k,m,ityp1,ityp2,ityp3)*cosph2(k)&
-              +eethet_nucl(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+            aux=ffthet_nucl(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+&
+             ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+&
+             ggthet_nucl(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+&
+             ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
             ethetai=ethetai+sinkt(m)*aux
             ethetai=ethetai+sinkt(m)*aux
-            dethetai=dethetai+0.5d0*m*aux*coskt(m)
-            dephii=dephii+k*sinkt(m)*(&
-               ccthet_nucl(k,m,ityp1,ityp2,ityp3)*cosph1(k)-&
-               bbthet_nucl(k,m,ityp1,ityp2,ityp3)*sinph1(k))
-            dephii1=dephii1+k*sinkt(m)*(&
-               eethet_nucl(k,m,ityp1,ityp2,ityp3)*cosph2(k)-&
-               ddthet_nucl(k,m,ityp1,ityp2,ityp3)*sinph2(k))
-            if (lprn) &
-           write (iout,*) "m",m," k",k," bbthet",&
-              bbthet_nucl(k,m,ityp1,ityp2,ityp3)," ccthet",&
-              ccthet_nucl(k,m,ityp1,ityp2,ityp3)," ddthet",&
-              ddthet_nucl(k,m,ityp1,ityp2,ityp3)," eethet",&
-              eethet_nucl(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
-          enddo
-        enddo
-        if (lprn) &
-        write(iout,*) "ethetai",ethetai
-        do m=1,ntheterm3_nucl
-          do k=2,ndouble_nucl
-            do l=1,k-1
-              aux=ffthet_nucl(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+&
-                 ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+&
-                 ggthet_nucl(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+&
-                 ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
-              ethetai=ethetai+sinkt(m)*aux
-              dethetai=dethetai+0.5d0*m*coskt(m)*aux
-              dephii=dephii+l*sinkt(m)*(&
-                -ffthet_nucl(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-&
-                 ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+&
-                 ggthet_nucl(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+&
-                 ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
-              dephii1=dephii1+(k-l)*sinkt(m)*( &
-                -ffthet_nucl(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+&
-                 ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+&
-                 ggthet_nucl(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-&
-                 ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
-              if (lprn) then
-              write (iout,*) "m",m," k",k," l",l," ffthet", &
-                 ffthet_nucl(l,k,m,ityp1,ityp2,ityp3), &
-                 ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)," ggthet",&
-                 ggthet_nucl(l,k,m,ityp1,ityp2,ityp3),&
-                 ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
-              write (iout,*) cosph1ph2(l,k)*sinkt(m), &
-                 cosph1ph2(k,l)*sinkt(m),&
-                 sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
-              endif
-            enddo
+            dethetai=dethetai+0.5d0*m*coskt(m)*aux
+            dephii=dephii+l*sinkt(m)*(&
+            -ffthet_nucl(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-&
+             ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+&
+             ggthet_nucl(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+&
+             ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+            dephii1=dephii1+(k-l)*sinkt(m)*( &
+            -ffthet_nucl(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+&
+             ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+&
+             ggthet_nucl(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-&
+             ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+            if (lprn) then
+            write (iout,*) "m",m," k",k," l",l," ffthet", &
+             ffthet_nucl(l,k,m,ityp1,ityp2,ityp3), &
+             ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)," ggthet",&
+             ggthet_nucl(l,k,m,ityp1,ityp2,ityp3),&
+             ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+            write (iout,*) cosph1ph2(l,k)*sinkt(m), &
+             cosph1ph2(k,l)*sinkt(m),&
+             sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
+            endif
           enddo
         enddo
           enddo
         enddo
+      enddo
 10      continue
 10      continue
-        if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)') &
-        i,theta(i)*rad2deg,phii*rad2deg, &
-        phii1*rad2deg,ethetai
-        etheta_nucl=etheta_nucl+ethetai
+      if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)') &
+      i,theta(i)*rad2deg,phii*rad2deg, &
+      phii1*rad2deg,ethetai
+      etheta_nucl=etheta_nucl+ethetai
 !        print *,i,"partial sum",etheta_nucl
 !        print *,i,"partial sum",etheta_nucl
-        if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang_nucl*dephii
-        if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang_nucl*dephii1
-        gloc(nphi+i-2,icg)=wang_nucl*dethetai
+      if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang_nucl*dephii
+      if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang_nucl*dephii1
+      gloc(nphi+i-2,icg)=wang_nucl*dethetai
       enddo
       return
       end subroutine ebend_nucl
       enddo
       return
       end subroutine ebend_nucl
@@ -21205,61 +20936,61 @@
 !el local variables
       integer :: i,j,iblock,itori,itori1
       real(kind=8) :: phii,gloci,v1ij,v2ij,cosphi,sinphi,&
 !el local variables
       integer :: i,j,iblock,itori,itori1
       real(kind=8) :: phii,gloci,v1ij,v2ij,cosphi,sinphi,&
-                   vl1ij,vl2ij,vl3ij,pom1,difi,etors_ii,pom
+               vl1ij,vl2ij,vl3ij,pom1,difi,etors_ii,pom
 ! Set lprn=.true. for debugging
       lprn=.false.
 !     lprn=.true.
       etors_nucl=0.0D0
 !      print *,"iphi_nucl_start/end", iphi_nucl_start,iphi_nucl_end
       do i=iphi_nucl_start,iphi_nucl_end
 ! Set lprn=.true. for debugging
       lprn=.false.
 !     lprn=.true.
       etors_nucl=0.0D0
 !      print *,"iphi_nucl_start/end", iphi_nucl_start,iphi_nucl_end
       do i=iphi_nucl_start,iphi_nucl_end
-        if (itype(i-2,2).eq.ntyp1_molec(2) .or. itype(i-1,2).eq.ntyp1_molec(2) &
-             .or. itype(i-3,2).eq.ntyp1_molec(2) &
-             .or. itype(i,2).eq.ntyp1_molec(2)) cycle
-        etors_ii=0.0D0
-        itori=itortyp_nucl(itype(i-2,2))
-        itori1=itortyp_nucl(itype(i-1,2))
-        phii=phi(i)
+      if (itype(i-2,2).eq.ntyp1_molec(2) .or. itype(i-1,2).eq.ntyp1_molec(2) &
+           .or. itype(i-3,2).eq.ntyp1_molec(2) &
+           .or. itype(i,2).eq.ntyp1_molec(2)) cycle
+      etors_ii=0.0D0
+      itori=itortyp_nucl(itype(i-2,2))
+      itori1=itortyp_nucl(itype(i-1,2))
+      phii=phi(i)
 !         print *,i,itori,itori1
 !         print *,i,itori,itori1
-        gloci=0.0D0
+      gloci=0.0D0
 !C Regular cosine and sine terms
 !C Regular cosine and sine terms
-        do j=1,nterm_nucl(itori,itori1)
-          v1ij=v1_nucl(j,itori,itori1)
-          v2ij=v2_nucl(j,itori,itori1)
-          cosphi=dcos(j*phii)
-          sinphi=dsin(j*phii)
-          etors_nucl=etors_nucl+v1ij*cosphi+v2ij*sinphi
-          if (energy_dec) etors_ii=etors_ii+&
-                     v1ij*cosphi+v2ij*sinphi
-          gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
-        enddo
+      do j=1,nterm_nucl(itori,itori1)
+        v1ij=v1_nucl(j,itori,itori1)
+        v2ij=v2_nucl(j,itori,itori1)
+        cosphi=dcos(j*phii)
+        sinphi=dsin(j*phii)
+        etors_nucl=etors_nucl+v1ij*cosphi+v2ij*sinphi
+        if (energy_dec) etors_ii=etors_ii+&
+                 v1ij*cosphi+v2ij*sinphi
+        gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
+      enddo
 !C Lorentz terms
 !C                         v1
 !C  E = SUM ----------------------------------- - v1
 !C          [v2 cos(phi/2)+v3 sin(phi/2)]^2 + 1
 !C
 !C Lorentz terms
 !C                         v1
 !C  E = SUM ----------------------------------- - v1
 !C          [v2 cos(phi/2)+v3 sin(phi/2)]^2 + 1
 !C
-        cosphi=dcos(0.5d0*phii)
-        sinphi=dsin(0.5d0*phii)
-        do j=1,nlor_nucl(itori,itori1)
-          vl1ij=vlor1_nucl(j,itori,itori1)
-          vl2ij=vlor2_nucl(j,itori,itori1)
-          vl3ij=vlor3_nucl(j,itori,itori1)
-          pom=vl2ij*cosphi+vl3ij*sinphi
-          pom1=1.0d0/(pom*pom+1.0d0)
-          etors_nucl=etors_nucl+vl1ij*pom1
-          if (energy_dec) etors_ii=etors_ii+ &
-                     vl1ij*pom1
-          pom=-pom*pom1*pom1
-          gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
-        enddo
+      cosphi=dcos(0.5d0*phii)
+      sinphi=dsin(0.5d0*phii)
+      do j=1,nlor_nucl(itori,itori1)
+        vl1ij=vlor1_nucl(j,itori,itori1)
+        vl2ij=vlor2_nucl(j,itori,itori1)
+        vl3ij=vlor3_nucl(j,itori,itori1)
+        pom=vl2ij*cosphi+vl3ij*sinphi
+        pom1=1.0d0/(pom*pom+1.0d0)
+        etors_nucl=etors_nucl+vl1ij*pom1
+        if (energy_dec) etors_ii=etors_ii+ &
+                 vl1ij*pom1
+        pom=-pom*pom1*pom1
+        gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
+      enddo
 !C Subtract the constant term
 !C Subtract the constant term
-        etors_nucl=etors_nucl-v0_nucl(itori,itori1)
-          if (energy_dec) write (iout,'(a6,i5,0pf7.3)') &
-              'etor',i,etors_ii-v0_nucl(itori,itori1)
-        if (lprn) &
+      etors_nucl=etors_nucl-v0_nucl(itori,itori1)
+        if (energy_dec) write (iout,'(a6,i5,0pf7.3)') &
+            'etor',i,etors_ii-v0_nucl(itori,itori1)
+      if (lprn) &
        write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') &
        restyp(itype(i-2,2),2),i-2,restyp(itype(i-1,2),2),i-1,itori,itori1, &
        (v1_nucl(j,itori,itori1),j=1,6),(v2_nucl(j,itori,itori1),j=1,6)
        write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') &
        restyp(itype(i-2,2),2),i-2,restyp(itype(i-1,2),2),i-1,itori,itori1, &
        (v1_nucl(j,itori,itori1),j=1,6),(v2_nucl(j,itori,itori1),j=1,6)
-        gloc(i-3,icg)=gloc(i-3,icg)+wtor_nucl*gloci
+      gloc(i-3,icg)=gloc(i-3,icg)+wtor_nucl*gloci
 !c       write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
       enddo
       return
 !c       write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
       enddo
       return
@@ -21274,12 +21005,13 @@
 !C the orientation of the CA-CA virtual bonds.
 !C 
       integer :: i,j,k,iteli,itelj,num_conti,isubchap,ind
 !C the orientation of the CA-CA virtual bonds.
 !C 
       integer :: i,j,k,iteli,itelj,num_conti,isubchap,ind
-      real(kind=8) :: dxi,dyi,dzi,dxj,dyj,dzj,aaa,bbb
+      real(kind=8) :: dxi,dyi,dzi,dxj,dyj,dzj,aaa,bbbi,sslipi,ssgradlipi, &
+                      sslipj,ssgradlipj,faclipij2
       real(kind=8) :: xj,yj,zj,rij,rrmij,sss,r3ij,r6ij,evdw1,&
       real(kind=8) :: xj,yj,zj,rij,rrmij,sss,r3ij,r6ij,evdw1,&
-                 dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,&
-                 dx_normj,dy_normj,dz_normj,rmij,ev1,ev2,evdwij,facvdw
+             dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,&
+             dx_normj,dy_normj,dz_normj,rmij,ev1,ev2,evdwij,facvdw
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
-                    dist_temp, dist_init,sss_grad,fac,evdw1ij
+                dist_temp, dist_init,sss_grad,fac,evdw1ij
       integer xshift,yshift,zshift
       real(kind=8),dimension(3):: ggg,gggp,gggm,erij
       real(kind=8) :: ees,eesij
       integer xshift,yshift,zshift
       real(kind=8),dimension(3):: ggg,gggp,gggm,erij
       real(kind=8) :: ees,eesij
@@ -21294,124 +21026,87 @@
 !c
 !      print *,"iatel_s_nucl,iatel_e_nucl",iatel_s_nucl,iatel_e_nucl
       do i=iatel_s_nucl,iatel_e_nucl
 !c
 !      print *,"iatel_s_nucl,iatel_e_nucl",iatel_s_nucl,iatel_e_nucl
       do i=iatel_s_nucl,iatel_e_nucl
-        if (itype(i,2).eq.ntyp1_molec(2) .or. itype(i+1,2).eq.ntyp1_molec(2)) cycle
-        dxi=dc(1,i)
-        dyi=dc(2,i)
-        dzi=dc(3,i)
-        dx_normi=dc_norm(1,i)
-        dy_normi=dc_norm(2,i)
-        dz_normi=dc_norm(3,i)
-        xmedi=c(1,i)+0.5d0*dxi
-        ymedi=c(2,i)+0.5d0*dyi
-        zmedi=c(3,i)+0.5d0*dzi
-          xmedi=dmod(xmedi,boxxsize)
-          if (xmedi.lt.0) xmedi=xmedi+boxxsize
-          ymedi=dmod(ymedi,boxysize)
-          if (ymedi.lt.0) ymedi=ymedi+boxysize
-          zmedi=dmod(zmedi,boxzsize)
-          if (zmedi.lt.0) zmedi=zmedi+boxzsize
-
-        do j=ielstart_nucl(i),ielend_nucl(i)
-          if (itype(j,2).eq.ntyp1_molec(2) .or. itype(j+1,2).eq.ntyp1_molec(2)) cycle
-          ind=ind+1
-          dxj=dc(1,j)
-          dyj=dc(2,j)
-          dzj=dc(3,j)
+      if (itype(i,2).eq.ntyp1_molec(2) .or. itype(i+1,2).eq.ntyp1_molec(2)) cycle
+      dxi=dc(1,i)
+      dyi=dc(2,i)
+      dzi=dc(3,i)
+      dx_normi=dc_norm(1,i)
+      dy_normi=dc_norm(2,i)
+      dz_normi=dc_norm(3,i)
+      xmedi=c(1,i)+0.5d0*dxi
+      ymedi=c(2,i)+0.5d0*dyi
+      zmedi=c(3,i)+0.5d0*dzi
+        call to_box(xmedi,ymedi,zmedi)
+        call lipid_layer(xmedi,ymedi,zmedi,sslipi,ssgradlipi)
+
+      do j=ielstart_nucl(i),ielend_nucl(i)
+        if (itype(j,2).eq.ntyp1_molec(2) .or. itype(j+1,2).eq.ntyp1_molec(2)) cycle
+        ind=ind+1
+        dxj=dc(1,j)
+        dyj=dc(2,j)
+        dzj=dc(3,j)
 !          xj=c(1,j)+0.5D0*dxj-xmedi
 !          yj=c(2,j)+0.5D0*dyj-ymedi
 !          zj=c(3,j)+0.5D0*dzj-zmedi
 !          xj=c(1,j)+0.5D0*dxj-xmedi
 !          yj=c(2,j)+0.5D0*dyj-ymedi
 !          zj=c(3,j)+0.5D0*dzj-zmedi
-          xj=c(1,j)+0.5D0*dxj
-          yj=c(2,j)+0.5D0*dyj
-          zj=c(3,j)+0.5D0*dzj
-          xj=mod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=mod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=mod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-      isubchap=0
-      dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
-      xj_safe=xj
-      yj_safe=yj
-      zj_safe=zj
-      do xshift=-1,1
-      do yshift=-1,1
-      do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            isubchap=1
-          endif
-       enddo
-       enddo
-       enddo
-       if (isubchap.eq.1) then
-!C          print *,i,j
-          xj=xj_temp-xmedi
-          yj=yj_temp-ymedi
-          zj=zj_temp-zmedi
-       else
-          xj=xj_safe-xmedi
-          yj=yj_safe-ymedi
-          zj=zj_safe-zmedi
-       endif
-
-          rij=xj*xj+yj*yj+zj*zj
+        xj=c(1,j)+0.5D0*dxj
+        yj=c(2,j)+0.5D0*dyj
+        zj=c(3,j)+0.5D0*dzj
+     call to_box(xj,yj,zj)
+     call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+      faclipij2=(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0
+      xj=boxshift(xj-xmedi,boxxsize)
+      yj=boxshift(yj-ymedi,boxysize)
+      zj=boxshift(zj-zmedi,boxzsize)
+        rij=xj*xj+yj*yj+zj*zj
 !c          write (2,*)"ij",i,j," r0pp",r0pp," rij",rij," epspp",epspp
 !c          write (2,*)"ij",i,j," r0pp",r0pp," rij",rij," epspp",epspp
-          fac=(r0pp**2/rij)**3
-          ev1=epspp*fac*fac
-          ev2=epspp*fac
-          evdw1ij=ev1-2*ev2
-          fac=(-ev1-evdw1ij)/rij
+        fac=(r0pp**2/rij)**3
+        ev1=epspp*fac*fac
+        ev2=epspp*fac
+        evdw1ij=ev1-2*ev2
+        fac=(-ev1-evdw1ij)/rij
 !          write (2,*)"fac",fac," ev1",ev1," ev2",ev2," evdw1ij",evdw1ij
 !          write (2,*)"fac",fac," ev1",ev1," ev2",ev2," evdw1ij",evdw1ij
-          if (energy_dec) write(iout,'(2i5,a9,f10.4)') i,j,"evdw1ij",evdw1ij
-          evdw1=evdw1+evdw1ij
+        if (energy_dec) write(iout,'(2i5,a9,f10.4)') i,j,"evdw1ij",evdw1ij
+        evdw1=evdw1+evdw1ij
 !C
 !C Calculate contributions to the Cartesian gradient.
 !C
 !C
 !C Calculate contributions to the Cartesian gradient.
 !C
-          ggg(1)=fac*xj
-          ggg(2)=fac*yj
-          ggg(3)=fac*zj
-          do k=1,3
-            gvdwpp_nucl(k,i)=gvdwpp_nucl(k,i)-ggg(k)
-            gvdwpp_nucl(k,j)=gvdwpp_nucl(k,j)+ggg(k)
-          enddo
+        ggg(1)=fac*xj
+        ggg(2)=fac*yj
+        ggg(3)=fac*zj
+        do k=1,3
+          gvdwpp_nucl(k,i)=gvdwpp_nucl(k,i)-ggg(k)
+          gvdwpp_nucl(k,j)=gvdwpp_nucl(k,j)+ggg(k)
+        enddo
 !c phoshate-phosphate electrostatic interactions
 !c phoshate-phosphate electrostatic interactions
-          rij=dsqrt(rij)
-          fac=1.0d0/rij
-          eesij=dexp(-BEES*rij)*fac
+        rij=dsqrt(rij)
+        fac=1.0d0/rij
+        eesij=dexp(-BEES*rij)*fac
 !          write (2,*)"fac",fac," eesijpp",eesij
 !          write (2,*)"fac",fac," eesijpp",eesij
-          if (energy_dec) write(iout,'(2i5,a9,f10.4)') i,j,"eesijpp",eesij
-          ees=ees+eesij
+        if (energy_dec) write(iout,'(2i5,a9,f10.4)') i,j,"eesijpp",eesij
+        ees=ees+eesij
 !c          fac=-eesij*fac
 !c          fac=-eesij*fac
-          fac=-(fac+BEES)*eesij*fac
-          ggg(1)=fac*xj
-          ggg(2)=fac*yj
-          ggg(3)=fac*zj
+        fac=-(fac+BEES)*eesij*fac
+        ggg(1)=fac*xj
+        ggg(2)=fac*yj
+        ggg(3)=fac*zj
 !c          write(2,*) "ggg",i,j,ggg(1),ggg(2),ggg(3)
 !c          write(2,*) "gelpp",i,(gelpp(k,i),k=1,3)
 !c          write(2,*) "gelpp",j,(gelpp(k,j),k=1,3)
 !c          write(2,*) "ggg",i,j,ggg(1),ggg(2),ggg(3)
 !c          write(2,*) "gelpp",i,(gelpp(k,i),k=1,3)
 !c          write(2,*) "gelpp",j,(gelpp(k,j),k=1,3)
-          do k=1,3
-            gelpp(k,i)=gelpp(k,i)-ggg(k)
-            gelpp(k,j)=gelpp(k,j)+ggg(k)
-          enddo
-        enddo ! j
+        do k=1,3
+          gelpp(k,i)=gelpp(k,i)-ggg(k)
+          gelpp(k,j)=gelpp(k,j)+ggg(k)
+        enddo
+      enddo ! j
       enddo   ! i
 !c      ees=332.0d0*ees 
       ees=AEES*ees
       do i=nnt,nct
 !c        write (2,*) "i",i," gelpp",(gelpp(k,i),k=1,3)
       enddo   ! i
 !c      ees=332.0d0*ees 
       ees=AEES*ees
       do i=nnt,nct
 !c        write (2,*) "i",i," gelpp",(gelpp(k,i),k=1,3)
-        do k=1,3
-          gvdwpp_nucl(k,i)=6*gvdwpp_nucl(k,i)
+      do k=1,3
+        gvdwpp_nucl(k,i)=6*gvdwpp_nucl(k,i)
 !c          gelpp(k,i)=332.0d0*gelpp(k,i)
 !c          gelpp(k,i)=332.0d0*gelpp(k,i)
-          gelpp(k,i)=AEES*gelpp(k,i)
-        enddo
+        gelpp(k,i)=AEES*gelpp(k,i)
+      enddo
 !c        write (2,*) "i",i," gelpp",(gelpp(k,i),k=1,3)
       enddo
 !c      write (2,*) "total EES",ees
 !c        write (2,*) "i",i," gelpp",(gelpp(k,i),k=1,3)
       enddo
 !c      write (2,*) "total EES",ees
@@ -21428,9 +21123,9 @@
       real(kind=8),dimension(3):: ggg
       integer :: i,iint,j,k,iteli,itypj,subchap
       real(kind=8) :: evdw2,evdw2_14,xi,yi,zi,xj,yj,zj,rrij,fac,&
       real(kind=8),dimension(3):: ggg
       integer :: i,iint,j,k,iteli,itypj,subchap
       real(kind=8) :: evdw2,evdw2_14,xi,yi,zi,xj,yj,zj,rrij,fac,&
-                   e1,e2,evdwij,rij,evdwpsb,eelpsb
+               e1,e2,evdwij,rij,evdwpsb,eelpsb
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
-                    dist_temp, dist_init
+                dist_temp, dist_init
       integer xshift,yshift,zshift
 
 !cd    print '(a)','Enter ESCP'
       integer xshift,yshift,zshift
 
 !cd    print '(a)','Enter ESCP'
@@ -21439,23 +21134,18 @@
       evdwpsb=0.0d0
 !      print *,"iatscp_s_nucl,iatscp_e_nucl",iatscp_s_nucl,iatscp_e_nucl
       do i=iatscp_s_nucl,iatscp_e_nucl
       evdwpsb=0.0d0
 !      print *,"iatscp_s_nucl,iatscp_e_nucl",iatscp_s_nucl,iatscp_e_nucl
       do i=iatscp_s_nucl,iatscp_e_nucl
-        if (itype(i,2).eq.ntyp1_molec(2) &
-         .or. itype(i+1,2).eq.ntyp1_molec(2)) cycle
-        xi=0.5D0*(c(1,i)+c(1,i+1))
-        yi=0.5D0*(c(2,i)+c(2,i+1))
-        zi=0.5D0*(c(3,i)+c(3,i+1))
-          xi=mod(xi,boxxsize)
-          if (xi.lt.0) xi=xi+boxxsize
-          yi=mod(yi,boxysize)
-          if (yi.lt.0) yi=yi+boxysize
-          zi=mod(zi,boxzsize)
-          if (zi.lt.0) zi=zi+boxzsize
-
-        do iint=1,nscp_gr_nucl(i)
-
-        do j=iscpstart_nucl(i,iint),iscpend_nucl(i,iint)
-          itypj=itype(j,2)
-          if (itypj.eq.ntyp1_molec(2)) cycle
+      if (itype(i,2).eq.ntyp1_molec(2) &
+       .or. itype(i+1,2).eq.ntyp1_molec(2)) cycle
+      xi=0.5D0*(c(1,i)+c(1,i+1))
+      yi=0.5D0*(c(2,i)+c(2,i+1))
+      zi=0.5D0*(c(3,i)+c(3,i+1))
+        call to_box(xi,yi,zi)
+
+      do iint=1,nscp_gr_nucl(i)
+
+      do j=iscpstart_nucl(i,iint),iscpend_nucl(i,iint)
+        itypj=itype(j,2)
+        if (itypj.eq.ntyp1_molec(2)) cycle
 !C Uncomment following three lines for SC-p interactions
 !c         xj=c(1,nres+j)-xi
 !c         yj=c(2,nres+j)-yi
 !C Uncomment following three lines for SC-p interactions
 !c         xj=c(1,nres+j)-xi
 !c         yj=c(2,nres+j)-yi
@@ -21464,79 +21154,48 @@
 !          xj=c(1,j)-xi
 !          yj=c(2,j)-yi
 !          zj=c(3,j)-zi
 !          xj=c(1,j)-xi
 !          yj=c(2,j)-yi
 !          zj=c(3,j)-zi
-          xj=c(1,j)
-          yj=c(2,j)
-          zj=c(3,j)
-          xj=mod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=mod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=mod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-      dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-      xj_safe=xj
-      yj_safe=yj
-      zj_safe=zj
-      subchap=0
-      do xshift=-1,1
-      do yshift=-1,1
-      do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-       enddo
-       enddo
-       enddo
-       if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-       else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-       endif
-
-          rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
-          fac=rrij**expon2
-          e1=fac*fac*aad_nucl(itypj)
-          e2=fac*bad_nucl(itypj)
-          if (iabs(j-i) .le. 2) then
-            e1=scal14*e1
-            e2=scal14*e2
-          endif
-          evdwij=e1+e2
-          evdwpsb=evdwpsb+evdwij
-          if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a4)') &
-             'evdw2',i,j,evdwij,"tu4"
+        xj=c(1,j)
+        yj=c(2,j)
+        zj=c(3,j)
+        call to_box(xj,yj,zj)
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)
+
+      dist_init=xj**2+yj**2+zj**2
+
+        rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+        fac=rrij**expon2
+        e1=fac*fac*aad_nucl(itypj)
+        e2=fac*bad_nucl(itypj)
+        if (iabs(j-i) .le. 2) then
+          e1=scal14*e1
+          e2=scal14*e2
+        endif
+        evdwij=e1+e2
+        evdwpsb=evdwpsb+evdwij
+        if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a4)') &
+           'evdw2',i,j,evdwij,"tu4"
 !C
 !C Calculate contributions to the gradient in the virtual-bond and SC vectors.
 !C
 !C
 !C Calculate contributions to the gradient in the virtual-bond and SC vectors.
 !C
-          fac=-(evdwij+e1)*rrij
-          ggg(1)=xj*fac
-          ggg(2)=yj*fac
-          ggg(3)=zj*fac
-          do k=1,3
-            gvdwpsb1(k,i)=gvdwpsb1(k,i)-ggg(k)
-            gvdwpsb(k,j)=gvdwpsb(k,j)+ggg(k)
-          enddo
+        fac=-(evdwij+e1)*rrij
+        ggg(1)=xj*fac
+        ggg(2)=yj*fac
+        ggg(3)=zj*fac
+        do k=1,3
+          gvdwpsb1(k,i)=gvdwpsb1(k,i)-ggg(k)
+          gvdwpsb(k,j)=gvdwpsb(k,j)+ggg(k)
         enddo
         enddo
+      enddo
 
 
-        enddo ! iint
+      enddo ! iint
       enddo ! i
       do i=1,nct
       enddo ! i
       do i=1,nct
-        do j=1,3
-          gvdwpsb(j,i)=expon*gvdwpsb(j,i)
-          gvdwpsb1(j,i)=expon*gvdwpsb1(j,i)
-        enddo
+      do j=1,3
+        gvdwpsb(j,i)=expon*gvdwpsb(j,i)
+        gvdwpsb1(j,i)=expon*gvdwpsb1(j,i)
+      enddo
       enddo
       return
       end subroutine epsb
       enddo
       return
       end subroutine epsb
@@ -21549,7 +21208,7 @@
       real(kind=8) :: xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
       real(kind=8) :: evdw,sig0iji,evdwsb,eelsb,ecorr,eelij
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
       real(kind=8) :: xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
       real(kind=8) :: evdw,sig0iji,evdwsb,eelsb,ecorr,eelij
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
-                    dist_temp, dist_init,aa,bb,faclip,sig0ij
+                dist_temp, dist_init,aa,bb,faclip,sig0ij
       integer :: ii
       logical lprn
       evdw=0.0D0
       integer :: ii
       logical lprn
       evdw=0.0D0
@@ -21560,160 +21219,127 @@
       ind=0
 !      print *,"iastsc_nucl",iatsc_s_nucl,iatsc_e_nucl
       do i=iatsc_s_nucl,iatsc_e_nucl
       ind=0
 !      print *,"iastsc_nucl",iatsc_s_nucl,iatsc_e_nucl
       do i=iatsc_s_nucl,iatsc_e_nucl
-        num_conti=0
-        num_conti2=0
-        itypi=itype(i,2)
+      num_conti=0
+      num_conti2=0
+      itypi=itype(i,2)
 !        PRINT *,"I=",i,itypi
 !        PRINT *,"I=",i,itypi
-        if (itypi.eq.ntyp1_molec(2)) cycle
-        itypi1=itype(i+1,2)
-        xi=c(1,nres+i)
-        yi=c(2,nres+i)
-        zi=c(3,nres+i)
-          xi=dmod(xi,boxxsize)
-          if (xi.lt.0) xi=xi+boxxsize
-          yi=dmod(yi,boxysize)
-          if (yi.lt.0) yi=yi+boxysize
-          zi=dmod(zi,boxzsize)
-          if (zi.lt.0) zi=zi+boxzsize
-
-        dxi=dc_norm(1,nres+i)
-        dyi=dc_norm(2,nres+i)
-        dzi=dc_norm(3,nres+i)
-        dsci_inv=vbld_inv(i+nres)
+      if (itypi.eq.ntyp1_molec(2)) cycle
+      itypi1=itype(i+1,2)
+      xi=c(1,nres+i)
+      yi=c(2,nres+i)
+      zi=c(3,nres+i)
+      call to_box(xi,yi,zi)
+      call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+      dxi=dc_norm(1,nres+i)
+      dyi=dc_norm(2,nres+i)
+      dzi=dc_norm(3,nres+i)
+      dsci_inv=vbld_inv(i+nres)
 !C
 !C Calculate SC interaction energy.
 !C
 !C
 !C Calculate SC interaction energy.
 !C
-        do iint=1,nint_gr_nucl(i)
+      do iint=1,nint_gr_nucl(i)
 !          print *,"tu?",i,istart_nucl(i,iint),iend_nucl(i,iint) 
 !          print *,"tu?",i,istart_nucl(i,iint),iend_nucl(i,iint) 
-          do j=istart_nucl(i,iint),iend_nucl(i,iint)
-            ind=ind+1
+        do j=istart_nucl(i,iint),iend_nucl(i,iint)
+          ind=ind+1
 !            print *,"JESTEM"
 !            print *,"JESTEM"
-            itypj=itype(j,2)
-            if (itypj.eq.ntyp1_molec(2)) cycle
-            dscj_inv=vbld_inv(j+nres)
-            sig0ij=sigma_nucl(itypi,itypj)
-            chi1=chi_nucl(itypi,itypj)
-            chi2=chi_nucl(itypj,itypi)
-            chi12=chi1*chi2
-            chip1=chip_nucl(itypi,itypj)
-            chip2=chip_nucl(itypj,itypi)
-            chip12=chip1*chip2
+          itypj=itype(j,2)
+          if (itypj.eq.ntyp1_molec(2)) cycle
+          dscj_inv=vbld_inv(j+nres)
+          sig0ij=sigma_nucl(itypi,itypj)
+          chi1=chi_nucl(itypi,itypj)
+          chi2=chi_nucl(itypj,itypi)
+          chi12=chi1*chi2
+          chip1=chip_nucl(itypi,itypj)
+          chip2=chip_nucl(itypj,itypi)
+          chip12=chip1*chip2
 !            xj=c(1,nres+j)-xi
 !            yj=c(2,nres+j)-yi
 !            zj=c(3,nres+j)-zi
 !            xj=c(1,nres+j)-xi
 !            yj=c(2,nres+j)-yi
 !            zj=c(3,nres+j)-zi
-           xj=c(1,nres+j)
-           yj=c(2,nres+j)
-           zj=c(3,nres+j)
-          xj=dmod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=dmod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=dmod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-      dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-      xj_safe=xj
-      yj_safe=yj
-      zj_safe=zj
-      subchap=0
-      do xshift=-1,1
-      do yshift=-1,1
-      do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-       enddo
-       enddo
-       enddo
-       if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-       else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-       endif
-
-            dxj=dc_norm(1,nres+j)
-            dyj=dc_norm(2,nres+j)
-            dzj=dc_norm(3,nres+j)
-            rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
-            rij=dsqrt(rrij)
+         xj=c(1,nres+j)
+         yj=c(2,nres+j)
+         zj=c(3,nres+j)
+     call to_box(xj,yj,zj)
+!     call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+!      aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+!       +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+!      bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+!       +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)
+
+          dxj=dc_norm(1,nres+j)
+          dyj=dc_norm(2,nres+j)
+          dzj=dc_norm(3,nres+j)
+          rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+          rij=dsqrt(rrij)
 !C Calculate angle-dependent terms of energy and contributions to their
 !C derivatives.
 !C Calculate angle-dependent terms of energy and contributions to their
 !C derivatives.
-            erij(1)=xj*rij
-            erij(2)=yj*rij
-            erij(3)=zj*rij
-            om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
-            om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
-            om12=dxi*dxj+dyi*dyj+dzi*dzj
-            call sc_angular_nucl
-            sigsq=1.0D0/sigsq
-            sig=sig0ij*dsqrt(sigsq)
-            rij_shift=1.0D0/rij-sig+sig0ij
+          erij(1)=xj*rij
+          erij(2)=yj*rij
+          erij(3)=zj*rij
+          om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
+          om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
+          om12=dxi*dxj+dyi*dyj+dzi*dzj
+          call sc_angular_nucl
+          sigsq=1.0D0/sigsq
+          sig=sig0ij*dsqrt(sigsq)
+          rij_shift=1.0D0/rij-sig+sig0ij
 !            print *,rij_shift,"rij_shift"
 !c            write (2,*) " rij",1.0D0/rij," sig",sig," sig0ij",sig0ij,
 !c     &       " rij_shift",rij_shift
 !            print *,rij_shift,"rij_shift"
 !c            write (2,*) " rij",1.0D0/rij," sig",sig," sig0ij",sig0ij,
 !c     &       " rij_shift",rij_shift
-            if (rij_shift.le.0.0D0) then
-              evdw=1.0D20
-              return
-            endif
-            sigder=-sig*sigsq
+          if (rij_shift.le.0.0D0) then
+            evdw=1.0D20
+            return
+          endif
+          sigder=-sig*sigsq
 !c---------------------------------------------------------------
 !c---------------------------------------------------------------
-            rij_shift=1.0D0/rij_shift
-            fac=rij_shift**expon
-            e1=fac*fac*aa_nucl(itypi,itypj)
-            e2=fac*bb_nucl(itypi,itypj)
-            evdwij=eps1*eps2rt*(e1+e2)
+          rij_shift=1.0D0/rij_shift
+          fac=rij_shift**expon
+          e1=fac*fac*aa_nucl(itypi,itypj)
+          e2=fac*bb_nucl(itypi,itypj)
+          evdwij=eps1*eps2rt*(e1+e2)
 !c            write (2,*) "eps1",eps1," eps2rt",eps2rt,
 !c     &       " e1",e1," e2",e2," evdwij",evdwij
 !c            write (2,*) "eps1",eps1," eps2rt",eps2rt,
 !c     &       " e1",e1," e2",e2," evdwij",evdwij
-            eps2der=evdwij
-            evdwij=evdwij*eps2rt
-            evdwsb=evdwsb+evdwij
-            if (lprn) then
-            sigm=dabs(aa_nucl(itypi,itypj)/bb_nucl(itypi,itypj))**(1.0D0/6.0D0)
-            epsi=bb_nucl(itypi,itypj)**2/aa_nucl(itypi,itypj)
-            write (iout,'(2(a3,i3,2x),17(0pf7.3))') &
-             restyp(itypi,2),i,restyp(itypj,2),j, &
-             epsi,sigm,chi1,chi2,chip1,chip2, &
-             eps1,eps2rt**2,sig,sig0ij, &
-             om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,&
-            evdwij
-            write (iout,*) "aa",aa_nucl(itypi,itypj)," bb",bb_nucl(itypi,itypj)
-            endif
+          eps2der=evdwij
+          evdwij=evdwij*eps2rt
+          evdwsb=evdwsb+evdwij
+          if (lprn) then
+          sigm=dabs(aa_nucl(itypi,itypj)/bb_nucl(itypi,itypj))**(1.0D0/6.0D0)
+          epsi=bb_nucl(itypi,itypj)**2/aa_nucl(itypi,itypj)
+          write (iout,'(2(a3,i3,2x),17(0pf7.3))') &
+           restyp(itypi,2),i,restyp(itypj,2),j, &
+           epsi,sigm,chi1,chi2,chip1,chip2, &
+           eps1,eps2rt**2,sig,sig0ij, &
+           om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,&
+          evdwij
+          write (iout,*) "aa",aa_nucl(itypi,itypj)," bb",bb_nucl(itypi,itypj)
+          endif
 
 
-            if (energy_dec) write (iout,'(a6,2i5,e15.3,a4)') &
-                             'evdw',i,j,evdwij,"tu3"
+          if (energy_dec) write (iout,'(a6,2i5,e15.3,a4)') &
+                       'evdw',i,j,evdwij,"tu3"
 
 
 !C Calculate gradient components.
 
 
 !C Calculate gradient components.
-            e1=e1*eps1*eps2rt**2
-            fac=-expon*(e1+evdwij)*rij_shift
-            sigder=fac*sigder
-            fac=rij*fac
+          e1=e1*eps1*eps2rt**2
+          fac=-expon*(e1+evdwij)*rij_shift
+          sigder=fac*sigder
+          fac=rij*fac
 !c            fac=0.0d0
 !C Calculate the radial part of the gradient
 !c            fac=0.0d0
 !C Calculate the radial part of the gradient
-            gg(1)=xj*fac
-            gg(2)=yj*fac
-            gg(3)=zj*fac
+          gg(1)=xj*fac
+          gg(2)=yj*fac
+          gg(3)=zj*fac
 !C Calculate angular part of the gradient.
 !C Calculate angular part of the gradient.
-            call sc_grad_nucl
-            call eelsbij(eelij,num_conti2)
-            if (energy_dec .and. &
-           (j.eq.i+1.or.j.eq.nres-i+1.or.j.eq.nres-i.or.j.eq.nres-i+2)) &
-          write (istat,'(e14.5)') evdwij
-            eelsb=eelsb+eelij
-          enddo      ! j
-        enddo        ! iint
-        num_cont_hb(i)=num_conti2
+          call sc_grad_nucl
+          call eelsbij(eelij,num_conti2)
+          if (energy_dec .and. &
+         (j.eq.i+1.or.j.eq.nres-i+1.or.j.eq.nres-i.or.j.eq.nres-i+2)) &
+        write (istat,'(e14.5)') evdwij
+          eelsb=eelsb+eelij
+        enddo      ! j
+      enddo        ! iint
+      num_cont_hb(i)=num_conti2
       enddo          ! i
 !c      write (iout,*) "Number of loop steps in EGB:",ind
 !cccc      energy_dec=.false.
       enddo          ! i
 !c      write (iout,*) "Number of loop steps in EGB:",ind
 !cccc      energy_dec=.false.
@@ -21726,7 +21352,7 @@
       real(kind=8),dimension(3) :: ggg,gggp,gggm,dcosb,dcosg
       real(kind=8),dimension(3,3) :: erder,uryg,urzg,vryg,vrzg
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
       real(kind=8),dimension(3) :: ggg,gggp,gggm,dcosb,dcosg
       real(kind=8),dimension(3,3) :: erder,uryg,urzg,vryg,vrzg
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
-                    dist_temp, dist_init,rlocshield,fracinbuf
+                dist_temp, dist_init,rlocshield,fracinbuf
       integer xshift,yshift,zshift,ilist,iresshield,num_conti2
 
 !c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions
       integer xshift,yshift,zshift,ilist,iresshield,num_conti2
 
 !c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions
@@ -21735,13 +21361,13 @@
       real(kind=8) :: ael6i,rrmij,rmij,r0ij,fcont,fprimcont,ees0tmp,facfac
       real(kind=8) :: ees,evdw1,eel_loc,aaa,bbb,ael3i,ael63i,ael32i
       real(kind=8) :: dx_normj,dy_normj,dz_normj,&
       real(kind=8) :: ael6i,rrmij,rmij,r0ij,fcont,fprimcont,ees0tmp,facfac
       real(kind=8) :: ees,evdw1,eel_loc,aaa,bbb,ael3i,ael63i,ael32i
       real(kind=8) :: dx_normj,dy_normj,dz_normj,&
-                  r3ij,r6ij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,fac5,fac6,&
-                  el1,el2,el3,el4,eesij,ees0ij,facvdw,facel,fac1,ecosa,&
-                  ecosb,ecosg,ury,urz,vry,vrz,facr,a22der,a23der,a32der,&
-                  a33der,eel_loc_ij,cosa4,wij,cosbg1,cosbg2,ees0pij,&
-                  ees0pij1,ees0mij,ees0mij1,fac3p,ees0mijp,ees0pijp,&
-                  ecosa1,ecosb1,ecosg1,ecosa2,ecosb2,ecosg2,ecosap,ecosbp,&
-                  ecosgp,ecosam,ecosbm,ecosgm,ghalf,itypi,itypj
+              r3ij,r6ij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,fac5,fac6,&
+              el1,el2,el3,el4,eesij,ees0ij,facvdw,facel,fac1,ecosa,&
+              ecosb,ecosg,ury,urz,vry,vrz,facr,a22der,a23der,a32der,&
+              a33der,eel_loc_ij,cosa4,wij,cosbg1,cosbg2,ees0pij,&
+              ees0pij1,ees0mij,ees0mij1,fac3p,ees0mijp,ees0pijp,&
+              ecosa1,ecosb1,ecosg1,ecosa2,ecosb2,ecosg2,ecosap,ecosbp,&
+              ecosgp,ecosam,ecosbm,ecosgm,ghalf,itypi,itypj
       ind=ind+1
       itypi=itype(i,2)
       itypj=itype(j,2)
       ind=ind+1
       itypi=itype(i,2)
       itypj=itype(j,2)
@@ -21765,13 +21391,13 @@
 !c      yj=c(2,j)+0.5D0*dyj-ymedi
 !c      zj=c(3,j)+0.5D0*dzj-zmedi
       if (ipot_nucl.ne.2) then
 !c      yj=c(2,j)+0.5D0*dyj-ymedi
 !c      zj=c(3,j)+0.5D0*dzj-zmedi
       if (ipot_nucl.ne.2) then
-        cosa=dx_normi*dx_normj+dy_normi*dy_normj+dz_normi*dz_normj
-        cosb=(xj*dx_normi+yj*dy_normi+zj*dz_normi)*rmij
-        cosg=(xj*dx_normj+yj*dy_normj+zj*dz_normj)*rmij
+      cosa=dx_normi*dx_normj+dy_normi*dy_normj+dz_normi*dz_normj
+      cosb=(xj*dx_normi+yj*dy_normi+zj*dz_normi)*rmij
+      cosg=(xj*dx_normj+yj*dy_normj+zj*dz_normj)*rmij
       else
       else
-        cosa=om12
-        cosb=om1
-        cosg=om2
+      cosa=om12
+      cosb=om1
+      cosg=om2
       endif
       r3ij=rij*rrij
       r6ij=r3ij*r3ij
       endif
       r3ij=rij*rrij
       r6ij=r3ij*r3ij
@@ -21793,12 +21419,12 @@
       ees0ij=4.0D0+facfac-fac1
 
       if (energy_dec) then
       ees0ij=4.0D0+facfac-fac1
 
       if (energy_dec) then
-          if(j.eq.i+1.or.j.eq.nres-i+1.or.j.eq.nres-i.or.j.eq.nres-i+2) &
-          write (istat,'(2a1,i4,1x,2a1,i4,4f10.5,3e12.5,$)') &
-           sugartyp(istype(i)),restyp(itypi,2),i,sugartyp(istype(j)),&
-           restyp(itypj,2),j,1.0d0/rij,cosa,cosb,cosg,fac*r3ij, &
-           (4.0D0+facfac-fac1)*r6ij,(2.0d0-2.0d0*facfac+fac1)*r6ij 
-          write (iout,'(a6,2i5,e15.3)') 'ees',i,j,eesij
+        if(j.eq.i+1.or.j.eq.nres-i+1.or.j.eq.nres-i.or.j.eq.nres-i+2) &
+        write (istat,'(2a1,i4,1x,2a1,i4,4f10.5,3e12.5,$)') &
+         sugartyp(istype(i)),restyp(itypi,2),i,sugartyp(istype(j)),&
+         restyp(itypj,2),j,1.0d0/rij,cosa,cosb,cosg,fac*r3ij, &
+         (4.0D0+facfac-fac1)*r6ij,(2.0d0-2.0d0*facfac+fac1)*r6ij 
+        write (iout,'(a6,2i5,e15.3)') 'ees',i,j,eesij
       endif
 
 !C
       endif
 
 !C
@@ -21816,10 +21442,10 @@
       ggg(2)=facel*yj
       ggg(3)=facel*zj
       do k=1,3
       ggg(2)=facel*yj
       ggg(3)=facel*zj
       do k=1,3
-        gelsbc(k,j)=gelsbc(k,j)+ggg(k)
-        gelsbc(k,i)=gelsbc(k,i)-ggg(k)
-        gelsbx(k,j)=gelsbx(k,j)+ggg(k)
-        gelsbx(k,i)=gelsbx(k,i)-ggg(k)
+      gelsbc(k,j)=gelsbc(k,j)+ggg(k)
+      gelsbc(k,i)=gelsbc(k,i)-ggg(k)
+      gelsbx(k,j)=gelsbx(k,j)+ggg(k)
+      gelsbx(k,i)=gelsbx(k,i)-ggg(k)
       enddo
 !*
 !* Angular part
       enddo
 !*
 !* Angular part
@@ -21834,123 +21460,123 @@
       ecosg=fac3*(fac1*cosb+cosg)+cosb*fac4+(cosg+2*fac1*cosb)*fac5+&
        fac6*fac1*cosb
       do k=1,3
       ecosg=fac3*(fac1*cosb+cosg)+cosb*fac4+(cosg+2*fac1*cosb)*fac5+&
        fac6*fac1*cosb
       do k=1,3
-        dcosb(k)=rij*(dc_norm(k,i+nres)-erij(k)*cosb)
-        dcosg(k)=rij*(dc_norm(k,j+nres)-erij(k)*cosg)
+      dcosb(k)=rij*(dc_norm(k,i+nres)-erij(k)*cosb)
+      dcosg(k)=rij*(dc_norm(k,j+nres)-erij(k)*cosg)
       enddo
       do k=1,3
       enddo
       do k=1,3
-        ggg(k)=ecosb*dcosb(k)+ecosg*dcosg(k)
+      ggg(k)=ecosb*dcosb(k)+ecosg*dcosg(k)
       enddo
       do k=1,3
       enddo
       do k=1,3
-        gelsbx(k,i)=gelsbx(k,i)-ggg(k) &
-             +(ecosa*(dc_norm(k,j+nres)-cosa*dc_norm(k,i+nres))&
-             + ecosb*(erij(k)-cosb*dc_norm(k,i+nres)))*vbld_inv(i+nres)
-        gelsbx(k,j)=gelsbx(k,j)+ggg(k) &
-             +(ecosa*(dc_norm(k,i+nres)-cosa*dc_norm(k,j+nres))&
-             + ecosg*(erij(k)-cosg*dc_norm(k,j+nres)))*vbld_inv(j+nres)
-        gelsbc(k,j)=gelsbc(k,j)+ggg(k)
-        gelsbc(k,i)=gelsbc(k,i)-ggg(k)
+      gelsbx(k,i)=gelsbx(k,i)-ggg(k) &
+           +(ecosa*(dc_norm(k,j+nres)-cosa*dc_norm(k,i+nres))&
+           + ecosb*(erij(k)-cosb*dc_norm(k,i+nres)))*vbld_inv(i+nres)
+      gelsbx(k,j)=gelsbx(k,j)+ggg(k) &
+           +(ecosa*(dc_norm(k,i+nres)-cosa*dc_norm(k,j+nres))&
+           + ecosg*(erij(k)-cosg*dc_norm(k,j+nres)))*vbld_inv(j+nres)
+      gelsbc(k,j)=gelsbc(k,j)+ggg(k)
+      gelsbc(k,i)=gelsbc(k,i)-ggg(k)
       enddo
 !      IF ( (wcorr_nucl.gt.0.0d0.or.wcorr3_nucl.gt.0.0d0) .and.
        IF ( j.gt.i+1 .and.&
       enddo
 !      IF ( (wcorr_nucl.gt.0.0d0.or.wcorr3_nucl.gt.0.0d0) .and.
        IF ( j.gt.i+1 .and.&
-          num_conti.le.maxconts) THEN
+        num_conti.le.maxcont) THEN
 !C
 !C Calculate the contact function. The ith column of the array JCONT will 
 !C contain the numbers of atoms that make contacts with the atom I (of numbers
 !C greater than I). The arrays FACONT and GACONT will contain the values of
 !C the contact function and its derivative.
 !C
 !C Calculate the contact function. The ith column of the array JCONT will 
 !C contain the numbers of atoms that make contacts with the atom I (of numbers
 !C greater than I). The arrays FACONT and GACONT will contain the values of
 !C the contact function and its derivative.
-        r0ij=2.20D0*sigma(itypi,itypj)
+      r0ij=2.20D0*sigma_nucl(itypi,itypj)
 !c        write (2,*) "ij",i,j," rij",1.0d0/rij," r0ij",r0ij
 !c        write (2,*) "ij",i,j," rij",1.0d0/rij," r0ij",r0ij
-        call gcont(rij,r0ij,1.0D0,0.2d0/r0ij,fcont,fprimcont)
+      call gcont(rij,r0ij,1.0D0,0.2d0/r0ij,fcont,fprimcont)
 !c        write (2,*) "fcont",fcont
 !c        write (2,*) "fcont",fcont
-        if (fcont.gt.0.0D0) then
-          num_conti=num_conti+1
-          num_conti2=num_conti2+1
+      if (fcont.gt.0.0D0) then
+        num_conti=num_conti+1
+        num_conti2=num_conti2+1
 
 
-          if (num_conti.gt.maxconts) then
-            write (iout,*) 'WARNING - max. # of contacts exceeded;',&
-                          ' will skip next contacts for this conf.'
-          else
-            jcont_hb(num_conti,i)=j
+        if (num_conti.gt.maxconts) then
+          write (iout,*) 'WARNING - max. # of contacts exceeded;',&
+                    ' will skip next contacts for this conf.',maxconts
+        else
+          jcont_hb(num_conti,i)=j
 !c            write (iout,*) "num_conti",num_conti,
 !c     &        " jcont_hb",jcont_hb(num_conti,i)
 !C Calculate contact energies
 !c            write (iout,*) "num_conti",num_conti,
 !c     &        " jcont_hb",jcont_hb(num_conti,i)
 !C Calculate contact energies
-            cosa4=4.0D0*cosa
-            wij=cosa-3.0D0*cosb*cosg
-            cosbg1=cosb+cosg
-            cosbg2=cosb-cosg
-            fac3=dsqrt(-ael6i)*r3ij
+          cosa4=4.0D0*cosa
+          wij=cosa-3.0D0*cosb*cosg
+          cosbg1=cosb+cosg
+          cosbg2=cosb-cosg
+          fac3=dsqrt(-ael6i)*r3ij
 !c            write (2,*) "ael6i",ael6i," r3ij",r3ij," fac3",fac3
 !c            write (2,*) "ael6i",ael6i," r3ij",r3ij," fac3",fac3
-            ees0tmp=4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1
-            if (ees0tmp.gt.0) then
-              ees0pij=dsqrt(ees0tmp)
-            else
-              ees0pij=0
-            endif
-            ees0tmp=4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2
-            if (ees0tmp.gt.0) then
-              ees0mij=dsqrt(ees0tmp)
-            else
-              ees0mij=0
-            endif
-            ees0p(num_conti,i)=0.5D0*fac3*(ees0pij+ees0mij)
-            ees0m(num_conti,i)=0.5D0*fac3*(ees0pij-ees0mij)
+          ees0tmp=4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1
+          if (ees0tmp.gt.0) then
+            ees0pij=dsqrt(ees0tmp)
+          else
+            ees0pij=0
+          endif
+          ees0tmp=4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2
+          if (ees0tmp.gt.0) then
+            ees0mij=dsqrt(ees0tmp)
+          else
+            ees0mij=0
+          endif
+          ees0p(num_conti,i)=0.5D0*fac3*(ees0pij+ees0mij)
+          ees0m(num_conti,i)=0.5D0*fac3*(ees0pij-ees0mij)
 !c            write (iout,*) "i",i," j",j,
 !c     &         " ees0m",ees0m(num_conti,i)," ees0p",ees0p(num_conti,i)
 !c            write (iout,*) "i",i," j",j,
 !c     &         " ees0m",ees0m(num_conti,i)," ees0p",ees0p(num_conti,i)
-            ees0pij1=fac3/ees0pij
-            ees0mij1=fac3/ees0mij
-            fac3p=-3.0D0*fac3*rrij
-            ees0pijp=0.5D0*fac3p*(ees0pij+ees0mij)
-            ees0mijp=0.5D0*fac3p*(ees0pij-ees0mij)
-            ecosa1=       ees0pij1*( 1.0D0+0.5D0*wij)
-            ecosb1=-1.5D0*ees0pij1*(wij*cosg+cosbg1)
-            ecosg1=-1.5D0*ees0pij1*(wij*cosb+cosbg1)
-            ecosa2=       ees0mij1*(-1.0D0+0.5D0*wij)
-            ecosb2=-1.5D0*ees0mij1*(wij*cosg+cosbg2)
-            ecosg2=-1.5D0*ees0mij1*(wij*cosb-cosbg2)
-            ecosap=ecosa1+ecosa2
-            ecosbp=ecosb1+ecosb2
-            ecosgp=ecosg1+ecosg2
-            ecosam=ecosa1-ecosa2
-            ecosbm=ecosb1-ecosb2
-            ecosgm=ecosg1-ecosg2
+          ees0pij1=fac3/ees0pij
+          ees0mij1=fac3/ees0mij
+          fac3p=-3.0D0*fac3*rrij
+          ees0pijp=0.5D0*fac3p*(ees0pij+ees0mij)
+          ees0mijp=0.5D0*fac3p*(ees0pij-ees0mij)
+          ecosa1=       ees0pij1*( 1.0D0+0.5D0*wij)
+          ecosb1=-1.5D0*ees0pij1*(wij*cosg+cosbg1)
+          ecosg1=-1.5D0*ees0pij1*(wij*cosb+cosbg1)
+          ecosa2=       ees0mij1*(-1.0D0+0.5D0*wij)
+          ecosb2=-1.5D0*ees0mij1*(wij*cosg+cosbg2)
+          ecosg2=-1.5D0*ees0mij1*(wij*cosb-cosbg2)
+          ecosap=ecosa1+ecosa2
+          ecosbp=ecosb1+ecosb2
+          ecosgp=ecosg1+ecosg2
+          ecosam=ecosa1-ecosa2
+          ecosbm=ecosb1-ecosb2
+          ecosgm=ecosg1-ecosg2
 !C End diagnostics
 !C End diagnostics
-            facont_hb(num_conti,i)=fcont
-            fprimcont=fprimcont/rij
-            do k=1,3
-              gggp(k)=ecosbp*dcosb(k)+ecosgp*dcosg(k)
-              gggm(k)=ecosbm*dcosb(k)+ecosgm*dcosg(k)
-            enddo
-            gggp(1)=gggp(1)+ees0pijp*xj
-            gggp(2)=gggp(2)+ees0pijp*yj
-            gggp(3)=gggp(3)+ees0pijp*zj
-            gggm(1)=gggm(1)+ees0mijp*xj
-            gggm(2)=gggm(2)+ees0mijp*yj
-            gggm(3)=gggm(3)+ees0mijp*zj
+          facont_hb(num_conti,i)=fcont
+          fprimcont=fprimcont/rij
+          do k=1,3
+            gggp(k)=ecosbp*dcosb(k)+ecosgp*dcosg(k)
+            gggm(k)=ecosbm*dcosb(k)+ecosgm*dcosg(k)
+          enddo
+          gggp(1)=gggp(1)+ees0pijp*xj
+          gggp(2)=gggp(2)+ees0pijp*yj
+          gggp(3)=gggp(3)+ees0pijp*zj
+          gggm(1)=gggm(1)+ees0mijp*xj
+          gggm(2)=gggm(2)+ees0mijp*yj
+          gggm(3)=gggm(3)+ees0mijp*zj
 !C Derivatives due to the contact function
 !C Derivatives due to the contact function
-            gacont_hbr(1,num_conti,i)=fprimcont*xj
-            gacont_hbr(2,num_conti,i)=fprimcont*yj
-            gacont_hbr(3,num_conti,i)=fprimcont*zj
-            do k=1,3
+          gacont_hbr(1,num_conti,i)=fprimcont*xj
+          gacont_hbr(2,num_conti,i)=fprimcont*yj
+          gacont_hbr(3,num_conti,i)=fprimcont*zj
+          do k=1,3
 !c
 !c Gradient of the correlation terms
 !c
 !c
 !c Gradient of the correlation terms
 !c
-              gacontp_hb1(k,num_conti,i)= &
-             (ecosap*(dc_norm(k,j+nres)-cosa*dc_norm(k,i+nres)) &
-            + ecosbp*(erij(k)-cosb*dc_norm(k,i+nres)))*vbld_inv(i+nres)
-              gacontp_hb2(k,num_conti,i)= &
-             (ecosap*(dc_norm(k,i+nres)-cosa*dc_norm(k,j+nres)) &
-            + ecosgp*(erij(k)-cosg*dc_norm(k,j+nres)))*vbld_inv(j+nres)
-              gacontp_hb3(k,num_conti,i)=gggp(k)
-              gacontm_hb1(k,num_conti,i)= &
-             (ecosam*(dc_norm(k,j+nres)-cosa*dc_norm(k,i+nres)) &
-            + ecosbm*(erij(k)-cosb*dc_norm(k,i+nres)))*vbld_inv(i+nres)
-              gacontm_hb2(k,num_conti,i)= &
-             (ecosam*(dc_norm(k,i+nres)-cosa*dc_norm(k,j+nres))&
-            + ecosgm*(erij(k)-cosg*dc_norm(k,j+nres)))*vbld_inv(j+nres)
-              gacontm_hb3(k,num_conti,i)=gggm(k)
-            enddo
-          endif
+            gacontp_hb1(k,num_conti,i)= &
+           (ecosap*(dc_norm(k,j+nres)-cosa*dc_norm(k,i+nres)) &
+          + ecosbp*(erij(k)-cosb*dc_norm(k,i+nres)))*vbld_inv(i+nres)
+            gacontp_hb2(k,num_conti,i)= &
+           (ecosap*(dc_norm(k,i+nres)-cosa*dc_norm(k,j+nres)) &
+          + ecosgp*(erij(k)-cosg*dc_norm(k,j+nres)))*vbld_inv(j+nres)
+            gacontp_hb3(k,num_conti,i)=gggp(k)
+            gacontm_hb1(k,num_conti,i)= &
+           (ecosam*(dc_norm(k,j+nres)-cosa*dc_norm(k,i+nres)) &
+          + ecosbm*(erij(k)-cosb*dc_norm(k,i+nres)))*vbld_inv(i+nres)
+            gacontm_hb2(k,num_conti,i)= &
+           (ecosam*(dc_norm(k,i+nres)-cosa*dc_norm(k,j+nres))&
+          + ecosgm*(erij(k)-cosg*dc_norm(k,j+nres)))*vbld_inv(j+nres)
+            gacontm_hb3(k,num_conti,i)=gggm(k)
+          enddo
         endif
         endif
+      endif
       ENDIF
       return
       end subroutine eelsbij
       ENDIF
       return
       end subroutine eelsbij
@@ -21963,26 +21589,26 @@
       eom2=eps2der*eps2rt_om2+sigder*sigsq_om2
       eom12=evdwij*eps1_om12+eps2der*eps2rt_om12+sigder*sigsq_om12
       do k=1,3
       eom2=eps2der*eps2rt_om2+sigder*sigsq_om2
       eom12=evdwij*eps1_om12+eps2der*eps2rt_om12+sigder*sigsq_om12
       do k=1,3
-        dcosom1(k)=rij*(dc_norm(k,nres+i)-om1*erij(k))
-        dcosom2(k)=rij*(dc_norm(k,nres+j)-om2*erij(k))
+      dcosom1(k)=rij*(dc_norm(k,nres+i)-om1*erij(k))
+      dcosom2(k)=rij*(dc_norm(k,nres+j)-om2*erij(k))
       enddo
       do k=1,3
       enddo
       do k=1,3
-        gg(k)=gg(k)+eom1*dcosom1(k)+eom2*dcosom2(k)
+      gg(k)=gg(k)+eom1*dcosom1(k)+eom2*dcosom2(k)
       enddo
       do k=1,3
       enddo
       do k=1,3
-        gvdwsbx(k,i)=gvdwsbx(k,i)-gg(k) &
-                 +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))&
-                 +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
-        gvdwsbx(k,j)=gvdwsbx(k,j)+gg(k) &
-                 +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
-                 +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+      gvdwsbx(k,i)=gvdwsbx(k,i)-gg(k) &
+             +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))&
+             +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+      gvdwsbx(k,j)=gvdwsbx(k,j)+gg(k) &
+             +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
+             +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
       enddo
 !C 
 !C Calculate the components of the gradient in DC and X
 !C
       do l=1,3
       enddo
 !C 
 !C Calculate the components of the gradient in DC and X
 !C
       do l=1,3
-        gvdwsbc(l,i)=gvdwsbc(l,i)-gg(l)
-        gvdwsbc(l,j)=gvdwsbc(l,j)+gg(l)
+      gvdwsbc(l,i)=gvdwsbc(l,i)-gg(l)
+      gvdwsbc(l,j)=gvdwsbc(l,j)+gg(l)
       enddo
       return
       end subroutine sc_grad_nucl
       enddo
       return
       end subroutine sc_grad_nucl
@@ -22007,126 +21633,126 @@
       delta=0.02d0*pi
       esbloc=0.0D0
       do i=loc_start_nucl,loc_end_nucl
       delta=0.02d0*pi
       esbloc=0.0D0
       do i=loc_start_nucl,loc_end_nucl
-        if (itype(i,2).eq.ntyp1_molec(2)) cycle
-        costtab(i+1) =dcos(theta(i+1))
-        sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
-        cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
-        sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
-        cosfac2=0.5d0/(1.0d0+costtab(i+1))
-        cosfac=dsqrt(cosfac2)
-        sinfac2=0.5d0/(1.0d0-costtab(i+1))
-        sinfac=dsqrt(sinfac2)
-        it=itype(i,2)
-        if (it.eq.10) goto 1
+      if (itype(i,2).eq.ntyp1_molec(2)) cycle
+      costtab(i+1) =dcos(theta(i+1))
+      sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
+      cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
+      sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
+      cosfac2=0.5d0/(1.0d0+costtab(i+1))
+      cosfac=dsqrt(cosfac2)
+      sinfac2=0.5d0/(1.0d0-costtab(i+1))
+      sinfac=dsqrt(sinfac2)
+      it=itype(i,2)
+      if (it.eq.10) goto 1
 
 !c
 !C  Compute the axes of tghe local cartesian coordinates system; store in
 !c   x_prime, y_prime and z_prime 
 !c
 
 !c
 !C  Compute the axes of tghe local cartesian coordinates system; store in
 !c   x_prime, y_prime and z_prime 
 !c
-        do j=1,3
-          x_prime(j) = 0.00
-          y_prime(j) = 0.00
-          z_prime(j) = 0.00
-        enddo
+      do j=1,3
+        x_prime(j) = 0.00
+        y_prime(j) = 0.00
+        z_prime(j) = 0.00
+      enddo
 !C        write(2,*) "dc_norm", dc_norm(1,i+nres),dc_norm(2,i+nres),
 !C     &   dc_norm(3,i+nres)
 !C        write(2,*) "dc_norm", dc_norm(1,i+nres),dc_norm(2,i+nres),
 !C     &   dc_norm(3,i+nres)
-        do j = 1,3
-          x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
-          y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
-        enddo
-        do j = 1,3
-          z_prime(j) = -uz(j,i-1)
+      do j = 1,3
+        x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
+        y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
+      enddo
+      do j = 1,3
+        z_prime(j) = -uz(j,i-1)
 !           z_prime(j)=0.0
 !           z_prime(j)=0.0
-        enddo
+      enddo
        
        
-        xx=0.0d0
-        yy=0.0d0
-        zz=0.0d0
-        do j = 1,3
-          xx = xx + x_prime(j)*dc_norm(j,i+nres)
-          yy = yy + y_prime(j)*dc_norm(j,i+nres)
-          zz = zz + z_prime(j)*dc_norm(j,i+nres)
-        enddo
+      xx=0.0d0
+      yy=0.0d0
+      zz=0.0d0
+      do j = 1,3
+        xx = xx + x_prime(j)*dc_norm(j,i+nres)
+        yy = yy + y_prime(j)*dc_norm(j,i+nres)
+        zz = zz + z_prime(j)*dc_norm(j,i+nres)
+      enddo
 
 
-        xxtab(i)=xx
-        yytab(i)=yy
-        zztab(i)=zz
-         it=itype(i,2)
-        do j = 1,9
-          x(j) = sc_parmin_nucl(j,it)
-        enddo
+      xxtab(i)=xx
+      yytab(i)=yy
+      zztab(i)=zz
+       it=itype(i,2)
+      do j = 1,9
+        x(j) = sc_parmin_nucl(j,it)
+      enddo
 #ifdef CHECK_COORD
 !Cc diagnostics - remove later
 #ifdef CHECK_COORD
 !Cc diagnostics - remove later
-        xx1 = dcos(alph(2))
-        yy1 = dsin(alph(2))*dcos(omeg(2))
-        zz1 = -dsin(alph(2))*dsin(omeg(2))
-        write(2,'(3f8.1,3f9.3,1x,3f9.3)') &
-         alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,&
-         xx1,yy1,zz1
+      xx1 = dcos(alph(2))
+      yy1 = dsin(alph(2))*dcos(omeg(2))
+      zz1 = -dsin(alph(2))*dsin(omeg(2))
+      write(2,'(3f8.1,3f9.3,1x,3f9.3)') &
+       alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,&
+       xx1,yy1,zz1
 !C,"  --- ", xx_w,yy_w,zz_w
 !c end diagnostics
 #endif
 !C,"  --- ", xx_w,yy_w,zz_w
 !c end diagnostics
 #endif
-        sumene = enesc_nucl(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
-        esbloc = esbloc + sumene
-        sumene2= enesc_nucl(x,xx,yy,0.0d0,cost2tab(i+1),sint2tab(i+1))
+      sumene = enesc_nucl(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
+      esbloc = esbloc + sumene
+      sumene2= enesc_nucl(x,xx,yy,0.0d0,cost2tab(i+1),sint2tab(i+1))
 !        print *,"enecomp",sumene,sumene2
 !        if (energy_dec) write(iout,*) "i",i," esbloc",sumene,esbloc,xx,yy,zz
 !        if (energy_dec) write(iout,*) "x",(x(k),k=1,9)
 #ifdef DEBUG
 !        print *,"enecomp",sumene,sumene2
 !        if (energy_dec) write(iout,*) "i",i," esbloc",sumene,esbloc,xx,yy,zz
 !        if (energy_dec) write(iout,*) "x",(x(k),k=1,9)
 #ifdef DEBUG
-        write (2,*) "x",(x(k),k=1,9)
+      write (2,*) "x",(x(k),k=1,9)
 !C
 !C This section to check the numerical derivatives of the energy of ith side
 !C chain in xx, yy, zz, and theta. Use the -DDEBUG compiler option or insert
 !C #define DEBUG in the code to turn it on.
 !C
 !C
 !C This section to check the numerical derivatives of the energy of ith side
 !C chain in xx, yy, zz, and theta. Use the -DDEBUG compiler option or insert
 !C #define DEBUG in the code to turn it on.
 !C
-        write (2,*) "sumene               =",sumene
-        aincr=1.0d-7
-        xxsave=xx
-        xx=xx+aincr
-        write (2,*) xx,yy,zz
-        sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
-        de_dxx_num=(sumenep-sumene)/aincr
-        xx=xxsave
-        write (2,*) "xx+ sumene from enesc=",sumenep,sumene
-        yysave=yy
-        yy=yy+aincr
-        write (2,*) xx,yy,zz
-        sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
-        de_dyy_num=(sumenep-sumene)/aincr
-        yy=yysave
-        write (2,*) "yy+ sumene from enesc=",sumenep,sumene
-        zzsave=zz
-        zz=zz+aincr
-        write (2,*) xx,yy,zz
-        sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
-        de_dzz_num=(sumenep-sumene)/aincr
-        zz=zzsave
-        write (2,*) "zz+ sumene from enesc=",sumenep,sumene
-        costsave=cost2tab(i+1)
-        sintsave=sint2tab(i+1)
-        cost2tab(i+1)=dcos(0.5d0*(theta(i+1)+aincr))
-        sint2tab(i+1)=dsin(0.5d0*(theta(i+1)+aincr))
-        sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
-        de_dt_num=(sumenep-sumene)/aincr
-        write (2,*) " t+ sumene from enesc=",sumenep,sumene
-        cost2tab(i+1)=costsave
-        sint2tab(i+1)=sintsave
+      write (2,*) "sumene               =",sumene
+      aincr=1.0d-7
+      xxsave=xx
+      xx=xx+aincr
+      write (2,*) xx,yy,zz
+      sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
+      de_dxx_num=(sumenep-sumene)/aincr
+      xx=xxsave
+      write (2,*) "xx+ sumene from enesc=",sumenep,sumene
+      yysave=yy
+      yy=yy+aincr
+      write (2,*) xx,yy,zz
+      sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
+      de_dyy_num=(sumenep-sumene)/aincr
+      yy=yysave
+      write (2,*) "yy+ sumene from enesc=",sumenep,sumene
+      zzsave=zz
+      zz=zz+aincr
+      write (2,*) xx,yy,zz
+      sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
+      de_dzz_num=(sumenep-sumene)/aincr
+      zz=zzsave
+      write (2,*) "zz+ sumene from enesc=",sumenep,sumene
+      costsave=cost2tab(i+1)
+      sintsave=sint2tab(i+1)
+      cost2tab(i+1)=dcos(0.5d0*(theta(i+1)+aincr))
+      sint2tab(i+1)=dsin(0.5d0*(theta(i+1)+aincr))
+      sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
+      de_dt_num=(sumenep-sumene)/aincr
+      write (2,*) " t+ sumene from enesc=",sumenep,sumene
+      cost2tab(i+1)=costsave
+      sint2tab(i+1)=sintsave
 !C End of diagnostics section.
 #endif
 !C        
 !C Compute the gradient of esc
 !C
 !C End of diagnostics section.
 #endif
 !C        
 !C Compute the gradient of esc
 !C
-        de_dxx=x(1)+2*x(4)*xx+x(7)*zz+x(8)*yy
-        de_dyy=x(2)+2*x(5)*yy+x(8)*xx+x(9)*zz
-        de_dzz=x(3)+2*x(6)*zz+x(7)*xx+x(9)*yy
-        de_dtt=0.0d0
+      de_dxx=x(1)+2*x(4)*xx+x(7)*zz+x(8)*yy
+      de_dyy=x(2)+2*x(5)*yy+x(8)*xx+x(9)*zz
+      de_dzz=x(3)+2*x(6)*zz+x(7)*xx+x(9)*yy
+      de_dtt=0.0d0
 #ifdef DEBUG
 #ifdef DEBUG
-        write (2,*) "x",(x(k),k=1,9)
-        write (2,*) "xx",xx," yy",yy," zz",zz
-        write (2,*) "de_xx   ",de_xx," de_yy   ",de_yy,&
-          " de_zz   ",de_zz," de_tt   ",de_tt
-        write (2,*) "de_xx_num",de_dxx_num," de_yy_num",de_dyy_num,&
-          " de_zz_num",de_dzz_num," de_dt_num",de_dt_num
+      write (2,*) "x",(x(k),k=1,9)
+      write (2,*) "xx",xx," yy",yy," zz",zz
+      write (2,*) "de_xx   ",de_xx," de_yy   ",de_yy,&
+        " de_zz   ",de_zz," de_tt   ",de_tt
+      write (2,*) "de_xx_num",de_dxx_num," de_yy_num",de_dyy_num,&
+        " de_zz_num",de_dzz_num," de_dt_num",de_dt_num
 #endif
 !C
        cossc=scalar(dc_norm(1,i),dc_norm(1,i+nres))
 #endif
 !C
        cossc=scalar(dc_norm(1,i),dc_norm(1,i+nres))
@@ -22134,45 +21760,45 @@
        cosfac2xx=cosfac2*xx
        sinfac2yy=sinfac2*yy
        do k = 1,3
        cosfac2xx=cosfac2*xx
        sinfac2yy=sinfac2*yy
        do k = 1,3
-         dt_dCi(k) = -(dc_norm(k,i-1)+costtab(i+1)*dc_norm(k,i))*&
-           vbld_inv(i+1)
-         dt_dCi1(k)= -(dc_norm(k,i)+costtab(i+1)*dc_norm(k,i-1))*&
-           vbld_inv(i)
-         pom=(dC_norm(k,i+nres)-cossc*dC_norm(k,i))*vbld_inv(i+1)
-         pom1=(dC_norm(k,i+nres)-cossc1*dC_norm(k,i-1))*vbld_inv(i)
+       dt_dCi(k) = -(dc_norm(k,i-1)+costtab(i+1)*dc_norm(k,i))*&
+         vbld_inv(i+1)
+       dt_dCi1(k)= -(dc_norm(k,i)+costtab(i+1)*dc_norm(k,i-1))*&
+         vbld_inv(i)
+       pom=(dC_norm(k,i+nres)-cossc*dC_norm(k,i))*vbld_inv(i+1)
+       pom1=(dC_norm(k,i+nres)-cossc1*dC_norm(k,i-1))*vbld_inv(i)
 !c         write (iout,*) "i",i," k",k," pom",pom," pom1",pom1,
 !c     &    " dt_dCi",dt_dCi(k)," dt_dCi1",dt_dCi1(k)
 !c         write (iout,*) "dC_norm",(dC_norm(j,i),j=1,3),
 !c     &   (dC_norm(j,i-1),j=1,3)," vbld_inv",vbld_inv(i+1),vbld_inv(i)
 !c         write (iout,*) "i",i," k",k," pom",pom," pom1",pom1,
 !c     &    " dt_dCi",dt_dCi(k)," dt_dCi1",dt_dCi1(k)
 !c         write (iout,*) "dC_norm",(dC_norm(j,i),j=1,3),
 !c     &   (dC_norm(j,i-1),j=1,3)," vbld_inv",vbld_inv(i+1),vbld_inv(i)
-         dXX_Ci(k)=pom*cosfac-dt_dCi(k)*cosfac2xx
-         dXX_Ci1(k)=-pom1*cosfac-dt_dCi1(k)*cosfac2xx
-         dYY_Ci(k)=pom*sinfac+dt_dCi(k)*sinfac2yy
-         dYY_Ci1(k)=pom1*sinfac+dt_dCi1(k)*sinfac2yy
-         dZZ_Ci1(k)=0.0d0
-         dZZ_Ci(k)=0.0d0
-         do j=1,3
-           dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
-           dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
-         enddo
+       dXX_Ci(k)=pom*cosfac-dt_dCi(k)*cosfac2xx
+       dXX_Ci1(k)=-pom1*cosfac-dt_dCi1(k)*cosfac2xx
+       dYY_Ci(k)=pom*sinfac+dt_dCi(k)*sinfac2yy
+       dYY_Ci1(k)=pom1*sinfac+dt_dCi1(k)*sinfac2yy
+       dZZ_Ci1(k)=0.0d0
+       dZZ_Ci(k)=0.0d0
+       do j=1,3
+         dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
+         dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+       enddo
 
 
-         dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
-         dYY_XYZ(k)=vbld_inv(i+nres)*(y_prime(k)-yy*dC_norm(k,i+nres))
-         dZZ_XYZ(k)=vbld_inv(i+nres)*(z_prime(k)-zz*dC_norm(k,i+nres))
+       dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
+       dYY_XYZ(k)=vbld_inv(i+nres)*(y_prime(k)-yy*dC_norm(k,i+nres))
+       dZZ_XYZ(k)=vbld_inv(i+nres)*(z_prime(k)-zz*dC_norm(k,i+nres))
 !c
 !c
-         dt_dCi(k) = -dt_dCi(k)/sinttab(i+1)
-         dt_dCi1(k)= -dt_dCi1(k)/sinttab(i+1)
+       dt_dCi(k) = -dt_dCi(k)/sinttab(i+1)
+       dt_dCi1(k)= -dt_dCi1(k)/sinttab(i+1)
        enddo
 
        do k=1,3
        enddo
 
        do k=1,3
-         dXX_Ctab(k,i)=dXX_Ci(k)
-         dXX_C1tab(k,i)=dXX_Ci1(k)
-         dYY_Ctab(k,i)=dYY_Ci(k)
-         dYY_C1tab(k,i)=dYY_Ci1(k)
-         dZZ_Ctab(k,i)=dZZ_Ci(k)
-         dZZ_C1tab(k,i)=dZZ_Ci1(k)
-         dXX_XYZtab(k,i)=dXX_XYZ(k)
-         dYY_XYZtab(k,i)=dYY_XYZ(k)
-         dZZ_XYZtab(k,i)=dZZ_XYZ(k)
+       dXX_Ctab(k,i)=dXX_Ci(k)
+       dXX_C1tab(k,i)=dXX_Ci1(k)
+       dYY_Ctab(k,i)=dYY_Ci(k)
+       dYY_C1tab(k,i)=dYY_Ci1(k)
+       dZZ_Ctab(k,i)=dZZ_Ci(k)
+       dZZ_C1tab(k,i)=dZZ_Ci1(k)
+       dXX_XYZtab(k,i)=dXX_XYZ(k)
+       dYY_XYZtab(k,i)=dYY_XYZ(k)
+       dZZ_XYZtab(k,i)=dZZ_XYZ(k)
        enddo
        do k = 1,3
 !c         write (iout,*) "k",k," dxx_ci1",dxx_ci1(k)," dyy_ci1",
        enddo
        do k = 1,3
 !c         write (iout,*) "k",k," dxx_ci1",dxx_ci1(k)," dyy_ci1",
@@ -22183,12 +21809,12 @@
 !c     &    dt_dci(k)
 !c         write (iout,*) "k",k," dxx_XYZ",dxx_XYZ(k)," dyy_XYZ",
 !c     &    dyy_XYZ(k)," dzz_XYZ",dzz_XYZ(k) 
 !c     &    dt_dci(k)
 !c         write (iout,*) "k",k," dxx_XYZ",dxx_XYZ(k)," dyy_XYZ",
 !c     &    dyy_XYZ(k)," dzz_XYZ",dzz_XYZ(k) 
-         gsbloc(k,i-1)=gsbloc(k,i-1)+(de_dxx*dxx_ci1(k) &
-         +de_dyy*dyy_ci1(k)+de_dzz*dzz_ci1(k)+de_dt*dt_dCi1(k))
-         gsbloc(k,i)=gsbloc(k,i)+(de_dxx*dxx_Ci(k) &
-         +de_dyy*dyy_Ci(k)+de_dzz*dzz_Ci(k)+de_dt*dt_dCi(k))
-         gsblocx(k,i)=                 de_dxx*dxx_XYZ(k)&
-         +de_dyy*dyy_XYZ(k)+de_dzz*dzz_XYZ(k)
+       gsbloc(k,i-1)=gsbloc(k,i-1)+(de_dxx*dxx_ci1(k) &
+       +de_dyy*dyy_ci1(k)+de_dzz*dzz_ci1(k)+de_dt*dt_dCi1(k))
+       gsbloc(k,i)=gsbloc(k,i)+(de_dxx*dxx_Ci(k) &
+       +de_dyy*dyy_Ci(k)+de_dzz*dzz_Ci(k)+de_dt*dt_dCi(k))
+       gsblocx(k,i)=                 de_dxx*dxx_XYZ(k)&
+       +de_dyy*dyy_XYZ(k)+de_dzz*dzz_XYZ(k)
 !         print *,i,de_dxx*dxx_ci1(k)+de_dyy*dyy_ci1(k),de_dzz*dzz_ci1(k)*2
        enddo
 !c       write(iout,*) "ENERGY GRAD = ", (gsbloc(k,i-1),k=1,3),
 !         print *,i,de_dxx*dxx_ci1(k)+de_dyy*dyy_ci1(k),de_dzz*dzz_ci1(k)*2
        enddo
 !c       write(iout,*) "ENERGY GRAD = ", (gsbloc(k,i-1),k=1,3),
@@ -22211,8 +21837,8 @@
 !c      write (2,*) "x",(x(i),i=1,9)
 !c      write(2,*)"xx",xx," yy",yy," zz",zz," cost2",cost2," sint2",sint2
       sumene=x(1)*xx+x(2)*yy+x(3)*zz+x(4)*xx**2 &
 !c      write (2,*) "x",(x(i),i=1,9)
 !c      write(2,*)"xx",xx," yy",yy," zz",zz," cost2",cost2," sint2",sint2
       sumene=x(1)*xx+x(2)*yy+x(3)*zz+x(4)*xx**2 &
-        + x(5)*yy**2+x(6)*zz**2+x(7)*xx*zz+x(8)*xx*yy &
-        + x(9)*yy*zz
+      + x(5)*yy**2+x(6)*zz**2+x(7)*xx*zz+x(8)*xx*yy &
+      + x(9)*yy*zz
       enesc_nucl=sumene
       return
       end function enesc_nucl
       enesc_nucl=sumene
       return
       end function enesc_nucl
@@ -22244,12 +21870,12 @@
 
       if (nfgtasks.le.1) goto 30
       if (lprn) then
 
       if (nfgtasks.le.1) goto 30
       if (lprn) then
-        write (iout,'(a)') 'Contact function values:'
-        do i=nnt,nct-1
-          write (iout,'(2i3,50(1x,i2,f5.2))')  &
-         i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i), &
-         j=1,num_cont_hb(i))
-        enddo
+      write (iout,'(a)') 'Contact function values:'
+      do i=nnt,nct-1
+        write (iout,'(2i3,50(1x,i2,f5.2))')  &
+       i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i), &
+       j=1,num_cont_hb(i))
+      enddo
       endif
 !C Caution! Following code assumes that electrostatic interactions concerning
 !C a given atom are split among at most two processors!
       endif
 !C Caution! Following code assumes that electrostatic interactions concerning
 !C a given atom are split among at most two processors!
@@ -22257,9 +21883,9 @@
       CorrelID=fg_rank+1
       ldone=.false.
       do i=1,max_cont
       CorrelID=fg_rank+1
       ldone=.false.
       do i=1,max_cont
-        do j=1,max_dim
-          buffer(i,j)=0.0D0
-        enddo
+      do j=1,max_dim
+        buffer(i,j)=0.0D0
+      enddo
       enddo
       mm=mod(fg_rank,2)
 !c      write (*,*) 'MyRank',MyRank,' mm',mm
       enddo
       mm=mod(fg_rank,2)
 !c      write (*,*) 'MyRank',MyRank,' mm',mm
@@ -22268,33 +21894,33 @@
 !c      write (*,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone
       if (fg_rank.gt.0) then
 !C Send correlation contributions to the preceding processor
 !c      write (*,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone
       if (fg_rank.gt.0) then
 !C Send correlation contributions to the preceding processor
-        msglen=msglen1
-        nn=num_cont_hb(iatel_s_nucl)
-        call pack_buffer(max_cont,max_dim,iatel_s,0,buffer)
+      msglen=msglen1
+      nn=num_cont_hb(iatel_s_nucl)
+      call pack_buffer(max_cont,max_dim,iatel_s,0,buffer)
 !c        write (*,*) 'The BUFFER array:'
 !c        do i=1,nn
 !c          write (*,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,30)
 !c        enddo
 !c        write (*,*) 'The BUFFER array:'
 !c        do i=1,nn
 !c          write (*,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,30)
 !c        enddo
-        if (ielstart_nucl(iatel_s_nucl).gt.iatel_s_nucl+ispp) then
-          msglen=msglen2
-          call pack_buffer(max_cont,max_dim,iatel_s+1,30,buffer)
+      if (ielstart_nucl(iatel_s_nucl).gt.iatel_s_nucl+ispp) then
+        msglen=msglen2
+        call pack_buffer(max_cont,max_dim,iatel_s+1,30,buffer)
 !C Clear the contacts of the atom passed to the neighboring processor
 !C Clear the contacts of the atom passed to the neighboring processor
-        nn=num_cont_hb(iatel_s_nucl+1)
+      nn=num_cont_hb(iatel_s_nucl+1)
 !c        do i=1,nn
 !c          write (*,'(i2,9(3f8.3,2x))') i,(buffer(i,j+30),j=1,30)
 !c        enddo
 !c        do i=1,nn
 !c          write (*,'(i2,9(3f8.3,2x))') i,(buffer(i,j+30),j=1,30)
 !c        enddo
-            num_cont_hb(iatel_s_nucl)=0
-        endif
+          num_cont_hb(iatel_s_nucl)=0
+      endif
 !cd      write (iout,*) 'Processor ',fg_rank,MyRank,
 !cd   & ' is sending correlation contribution to processor',fg_rank-1,
 !cd   & ' msglen=',msglen
 !c        write (*,*) 'Processor ',fg_rank,MyRank,
 !c     & ' is sending correlation contribution to processor',fg_rank-1,
 !c     & ' msglen=',msglen,' CorrelType=',CorrelType
 !cd      write (iout,*) 'Processor ',fg_rank,MyRank,
 !cd   & ' is sending correlation contribution to processor',fg_rank-1,
 !cd   & ' msglen=',msglen
 !c        write (*,*) 'Processor ',fg_rank,MyRank,
 !c     & ' is sending correlation contribution to processor',fg_rank-1,
 !c     & ' msglen=',msglen,' CorrelType=',CorrelType
-        time00=MPI_Wtime()
-        call MPI_Send(buffer,msglen,MPI_DOUBLE_PRECISION,fg_rank-1, &
-         CorrelType,FG_COMM,IERROR)
-        time_sendrecv=time_sendrecv+MPI_Wtime()-time00
+      time00=MPI_Wtime()
+      call MPI_Send(buffer,msglen,MPI_DOUBLE_PRECISION,fg_rank-1, &
+       CorrelType,FG_COMM,IERROR)
+      time_sendrecv=time_sendrecv+MPI_Wtime()-time00
 !cd      write (iout,*) 'Processor ',fg_rank,
 !cd   & ' has sent correlation contribution to processor',fg_rank-1,
 !cd   & ' msglen=',msglen,' CorrelID=',CorrelID
 !cd      write (iout,*) 'Processor ',fg_rank,
 !cd   & ' has sent correlation contribution to processor',fg_rank-1,
 !cd   & ' msglen=',msglen,' CorrelID=',CorrelID
@@ -22309,24 +21935,24 @@
 !c      write (*,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone
       if (fg_rank.lt.nfgtasks-1) then
 !C Receive correlation contributions from the next processor
 !c      write (*,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone
       if (fg_rank.lt.nfgtasks-1) then
 !C Receive correlation contributions from the next processor
-        msglen=msglen1
-        if (ielend_nucl(iatel_e_nucl).lt.nct_molec(2)-1) msglen=msglen2
+      msglen=msglen1
+      if (ielend_nucl(iatel_e_nucl).lt.nct_molec(2)-1) msglen=msglen2
 !cd      write (iout,*) 'Processor',fg_rank,
 !cd   & ' is receiving correlation contribution from processor',fg_rank+1,
 !cd   & ' msglen=',msglen,' CorrelType=',CorrelType
 !c        write (*,*) 'Processor',fg_rank,
 !c     &' is receiving correlation contribution from processor',fg_rank+1,
 !c     & ' msglen=',msglen,' CorrelType=',CorrelType
 !cd      write (iout,*) 'Processor',fg_rank,
 !cd   & ' is receiving correlation contribution from processor',fg_rank+1,
 !cd   & ' msglen=',msglen,' CorrelType=',CorrelType
 !c        write (*,*) 'Processor',fg_rank,
 !c     &' is receiving correlation contribution from processor',fg_rank+1,
 !c     & ' msglen=',msglen,' CorrelType=',CorrelType
-        time00=MPI_Wtime()
-        nbytes=-1
-        do while (nbytes.le.0)
-          call MPI_Probe(fg_rank+1,CorrelType,FG_COMM,status,IERROR)
-          call MPI_Get_count(status,MPI_DOUBLE_PRECISION,nbytes,IERROR)
-        enddo
+      time00=MPI_Wtime()
+      nbytes=-1
+      do while (nbytes.le.0)
+        call MPI_Probe(fg_rank+1,CorrelType,FG_COMM,status,IERROR)
+        call MPI_Get_count(status,MPI_DOUBLE_PRECISION,nbytes,IERROR)
+      enddo
 !c        print *,'Processor',myrank,' msglen',msglen,' nbytes',nbytes
 !c        print *,'Processor',myrank,' msglen',msglen,' nbytes',nbytes
-        call MPI_Recv(buffer,nbytes,MPI_DOUBLE_PRECISION, &
-         fg_rank+1,CorrelType,FG_COMM,status,IERROR)
-        time_sendrecv=time_sendrecv+MPI_Wtime()-time00
+      call MPI_Recv(buffer,nbytes,MPI_DOUBLE_PRECISION, &
+       fg_rank+1,CorrelType,FG_COMM,status,IERROR)
+      time_sendrecv=time_sendrecv+MPI_Wtime()-time00
 !c        write (*,*) 'Processor',fg_rank,
 !c     &' has received correlation contribution from processor',fg_rank+1,
 !c     & ' msglen=',msglen,' nbytes=',nbytes
 !c        write (*,*) 'Processor',fg_rank,
 !c     &' has received correlation contribution from processor',fg_rank+1,
 !c     & ' msglen=',msglen,' nbytes=',nbytes
@@ -22334,18 +21960,18 @@
 !c        do i=1,max_cont
 !c          write (*,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,60)
 !c        enddo
 !c        do i=1,max_cont
 !c          write (*,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,60)
 !c        enddo
-        if (msglen.eq.msglen1) then
-          call unpack_buffer(max_cont,max_dim,iatel_e_nucl+1,0,buffer)
-        else if (msglen.eq.msglen2)  then
-          call unpack_buffer(max_cont,max_dim,iatel_e_nucl,0,buffer)
-          call unpack_buffer(max_cont,max_dim,iatel_e_nucl+1,30,buffer)
-        else
-          write (iout,*) &
+      if (msglen.eq.msglen1) then
+        call unpack_buffer(max_cont,max_dim,iatel_e_nucl+1,0,buffer)
+      else if (msglen.eq.msglen2)  then
+        call unpack_buffer(max_cont,max_dim,iatel_e_nucl,0,buffer)
+        call unpack_buffer(max_cont,max_dim,iatel_e_nucl+1,30,buffer)
+      else
+        write (iout,*) &
       'ERROR!!!! message length changed while processing correlations.'
       'ERROR!!!! message length changed while processing correlations.'
-          write (*,*) &
+        write (*,*) &
       'ERROR!!!! message length changed while processing correlations.'
       'ERROR!!!! message length changed while processing correlations.'
-          call MPI_Abort(MPI_COMM_WORLD,Error,IERROR)
-        endif ! msglen.eq.msglen1
+        call MPI_Abort(MPI_COMM_WORLD,Error,IERROR)
+      endif ! msglen.eq.msglen1
       endif ! fg_rank.lt.nfgtasks-1
       if (ldone) goto 30
       ldone=.true.
       endif ! fg_rank.lt.nfgtasks-1
       if (ldone) goto 30
       ldone=.true.
@@ -22353,12 +21979,12 @@
    30 continue
 #endif
       if (lprn) then
    30 continue
 #endif
       if (lprn) then
-        write (iout,'(a)') 'Contact function values:'
-        do i=nnt_molec(2),nct_molec(2)-1
-          write (iout,'(2i3,50(1x,i2,f5.2))') &
-         i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i), &
-         j=1,num_cont_hb(i))
-        enddo
+      write (iout,'(a)') 'Contact function values:'
+      do i=nnt_molec(2),nct_molec(2)-1
+        write (iout,'(2i3,50(1x,i2,f5.2))') &
+       i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i), &
+       j=1,num_cont_hb(i))
+      enddo
       endif
       ecorr=0.0D0
       ecorr3=0.0d0
       endif
       ecorr=0.0D0
       ecorr3=0.0d0
@@ -22374,17 +22000,17 @@
 !      print *,"iatsc_s_nucl,iatsc_e_nucl",iatsc_s_nucl,iatsc_e_nucl
 !C Calculate the local-electrostatic correlation terms
       do i=iatsc_s_nucl,iatsc_e_nucl
 !      print *,"iatsc_s_nucl,iatsc_e_nucl",iatsc_s_nucl,iatsc_e_nucl
 !C Calculate the local-electrostatic correlation terms
       do i=iatsc_s_nucl,iatsc_e_nucl
-        i1=i+1
-        num_conti=num_cont_hb(i)
-        num_conti1=num_cont_hb(i+1)
+      i1=i+1
+      num_conti=num_cont_hb(i)
+      num_conti1=num_cont_hb(i+1)
 !        print *,i,num_conti,num_conti1
 !        print *,i,num_conti,num_conti1
-        do jj=1,num_conti
-          j=jcont_hb(jj,i)
-          do kk=1,num_conti1
-            j1=jcont_hb(kk,i1)
+      do jj=1,num_conti
+        j=jcont_hb(jj,i)
+        do kk=1,num_conti1
+          j1=jcont_hb(kk,i1)
 !c            write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
 !c     &         ' jj=',jj,' kk=',kk
 !c            write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
 !c     &         ' jj=',jj,' kk=',kk
-            if (j1.eq.j+1 .or. j1.eq.j-1) then
+          if (j1.eq.j+1 .or. j1.eq.j-1) then
 !C
 !C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously. 
 !C The system gains extra energy.
 !C
 !C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously. 
 !C The system gains extra energy.
@@ -22392,11 +22018,11 @@
 !C parallel dipoles of stacknig bases and sin(mui)sin(muj)/eps/d^3=0.7
 !C Need to implement full formulas 34 and 35 from Liwo et al., 1998.
 !C
 !C parallel dipoles of stacknig bases and sin(mui)sin(muj)/eps/d^3=0.7
 !C Need to implement full formulas 34 and 35 from Liwo et al., 1998.
 !C
-              ecorr=ecorr+ehbcorr_nucl(i,j,i+1,j1,jj,kk,0.528D0,0.132D0)
-              if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') &
-                 'ecorrh',i,j,ehbcorr_nucl(i,j,i+1,j1,jj,kk,0.528D0,0.132D0) 
-              n_corr=n_corr+1
-            else if (j1.eq.j) then
+            ecorr=ecorr+ehbcorr_nucl(i,j,i+1,j1,jj,kk,0.528D0,0.132D0)
+            if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') &
+             'ecorrh',i,j,ehbcorr_nucl(i,j,i+1,j1,jj,kk,0.528D0,0.132D0) 
+            n_corr=n_corr+1
+          else if (j1.eq.j) then
 !C
 !C Contacts I-J and I-(J+1) occur simultaneously. 
 !C The system loses extra energy.
 !C
 !C Contacts I-J and I-(J+1) occur simultaneously. 
 !C The system loses extra energy.
@@ -22406,20 +22032,20 @@
 !C
 !c              write (iout,*) 'ecorr3: i=',i,' j=',j,' i1=',i1,' j1=',j1,
 !c     &         ' jj=',jj,' kk=',kk
 !C
 !c              write (iout,*) 'ecorr3: i=',i,' j=',j,' i1=',i1,' j1=',j1,
 !c     &         ' jj=',jj,' kk=',kk
-              ecorr3=ecorr3+ehbcorr3_nucl(i,j,i+1,j,jj,kk,0.310D0,-0.155D0)
-            endif
-          enddo ! kk
-          do kk=1,num_conti
-            j1=jcont_hb(kk,i)
+            ecorr3=ecorr3+ehbcorr3_nucl(i,j,i+1,j,jj,kk,0.310D0,-0.155D0)
+          endif
+        enddo ! kk
+        do kk=1,num_conti
+          j1=jcont_hb(kk,i)
 !c            write (iout,*) 'ecorr3: i=',i,' j=',j,' i1=',i1,' j1=',j1,
 !c     &         ' jj=',jj,' kk=',kk
 !c            write (iout,*) 'ecorr3: i=',i,' j=',j,' i1=',i1,' j1=',j1,
 !c     &         ' jj=',jj,' kk=',kk
-            if (j1.eq.j+1) then
+          if (j1.eq.j+1) then
 !C Contacts I-J and (I+1)-J occur simultaneously. 
 !C The system loses extra energy.
 !C Contacts I-J and (I+1)-J occur simultaneously. 
 !C The system loses extra energy.
-              ecorr3=ecorr3+ehbcorr3_nucl(i,j,i,j+1,jj,kk,0.310D0,-0.155D0)
-            endif ! j1==j+1
-          enddo ! kk
-        enddo ! jj
+            ecorr3=ecorr3+ehbcorr3_nucl(i,j,i,j+1,jj,kk,0.310D0,-0.155D0)
+          endif ! j1==j+1
+        enddo ! kk
+      enddo ! jj
       enddo ! i
       return
       end subroutine multibody_hb_nucl
       enddo ! i
       return
       end subroutine multibody_hb_nucl
@@ -22436,9 +22062,9 @@
 !el local variables
       integer :: i,j,k,l,jj,kk,ll,ilist,m, iresshield
       real(kind=8) :: coeffp,coeffm,eij,ekl,ees0pij,ees0pkl,ees0mij,&
 !el local variables
       integer :: i,j,k,l,jj,kk,ll,ilist,m, iresshield
       real(kind=8) :: coeffp,coeffm,eij,ekl,ees0pij,ees0pkl,ees0mij,&
-                   ees0mkl,ees,coeffpees0pij,coeffmees0mij,&
-                   coeffpees0pkl,coeffmees0mkl,gradlongij,gradlongkl, &
-                   rlocshield
+               ees0mkl,ees,coeffpees0pij,coeffmees0mij,&
+               coeffpees0pkl,coeffmees0mkl,gradlongij,gradlongkl, &
+               rlocshield
 
       lprn=.false.
       eij=facont_hb(jj,i)
 
       lprn=.false.
       eij=facont_hb(jj,i)
@@ -22467,32 +22093,32 @@
       coeffpees0pkl=coeffp*ees0pkl
       coeffmees0mkl=coeffm*ees0mkl
       do ll=1,3
       coeffpees0pkl=coeffp*ees0pkl
       coeffmees0mkl=coeffm*ees0mkl
       do ll=1,3
-        gradxorr_nucl(ll,i)=gradxorr_nucl(ll,i) &
+      gradxorr_nucl(ll,i)=gradxorr_nucl(ll,i) &
        -ekont*(coeffpees0pkl*gacontp_hb1(ll,jj,i)+&
        coeffmees0mkl*gacontm_hb1(ll,jj,i))
        -ekont*(coeffpees0pkl*gacontp_hb1(ll,jj,i)+&
        coeffmees0mkl*gacontm_hb1(ll,jj,i))
-        gradxorr_nucl(ll,j)=gradxorr_nucl(ll,j) &
-        -ekont*(coeffpees0pkl*gacontp_hb2(ll,jj,i)+&
-        coeffmees0mkl*gacontm_hb2(ll,jj,i))
-        gradxorr_nucl(ll,k)=gradxorr_nucl(ll,k) &
-        -ekont*(coeffpees0pij*gacontp_hb1(ll,kk,k)+&
-        coeffmees0mij*gacontm_hb1(ll,kk,k))
-        gradxorr_nucl(ll,l)=gradxorr_nucl(ll,l) &
-        -ekont*(coeffpees0pij*gacontp_hb2(ll,kk,k)+ &
-        coeffmees0mij*gacontm_hb2(ll,kk,k))
-        gradlongij=ees*ekl*gacont_hbr(ll,jj,i)- &
-          ekont*(coeffpees0pkl*gacontp_hb3(ll,jj,i)+ &
-          coeffmees0mkl*gacontm_hb3(ll,jj,i))
-        gradcorr_nucl(ll,j)=gradcorr_nucl(ll,j)+gradlongij
-        gradcorr_nucl(ll,i)=gradcorr_nucl(ll,i)-gradlongij
-        gradlongkl=ees*eij*gacont_hbr(ll,kk,k)- &
-          ekont*(coeffpees0pij*gacontp_hb3(ll,kk,k)+ &
-          coeffmees0mij*gacontm_hb3(ll,kk,k))
-        gradcorr_nucl(ll,l)=gradcorr_nucl(ll,l)+gradlongkl
-        gradcorr_nucl(ll,k)=gradcorr_nucl(ll,k)-gradlongkl
-        gradxorr_nucl(ll,i)=gradxorr_nucl(ll,i)-gradlongij
-        gradxorr_nucl(ll,j)=gradxorr_nucl(ll,j)+gradlongij
-        gradxorr_nucl(ll,k)=gradxorr_nucl(ll,k)-gradlongkl
-        gradxorr_nucl(ll,l)=gradxorr_nucl(ll,l)+gradlongkl
+      gradxorr_nucl(ll,j)=gradxorr_nucl(ll,j) &
+      -ekont*(coeffpees0pkl*gacontp_hb2(ll,jj,i)+&
+      coeffmees0mkl*gacontm_hb2(ll,jj,i))
+      gradxorr_nucl(ll,k)=gradxorr_nucl(ll,k) &
+      -ekont*(coeffpees0pij*gacontp_hb1(ll,kk,k)+&
+      coeffmees0mij*gacontm_hb1(ll,kk,k))
+      gradxorr_nucl(ll,l)=gradxorr_nucl(ll,l) &
+      -ekont*(coeffpees0pij*gacontp_hb2(ll,kk,k)+ &
+      coeffmees0mij*gacontm_hb2(ll,kk,k))
+      gradlongij=ees*ekl*gacont_hbr(ll,jj,i)- &
+        ekont*(coeffpees0pkl*gacontp_hb3(ll,jj,i)+ &
+        coeffmees0mkl*gacontm_hb3(ll,jj,i))
+      gradcorr_nucl(ll,j)=gradcorr_nucl(ll,j)+gradlongij
+      gradcorr_nucl(ll,i)=gradcorr_nucl(ll,i)-gradlongij
+      gradlongkl=ees*eij*gacont_hbr(ll,kk,k)- &
+        ekont*(coeffpees0pij*gacontp_hb3(ll,kk,k)+ &
+        coeffmees0mij*gacontm_hb3(ll,kk,k))
+      gradcorr_nucl(ll,l)=gradcorr_nucl(ll,l)+gradlongkl
+      gradcorr_nucl(ll,k)=gradcorr_nucl(ll,k)-gradlongkl
+      gradxorr_nucl(ll,i)=gradxorr_nucl(ll,i)-gradlongij
+      gradxorr_nucl(ll,j)=gradxorr_nucl(ll,j)+gradlongij
+      gradxorr_nucl(ll,k)=gradxorr_nucl(ll,k)-gradlongkl
+      gradxorr_nucl(ll,l)=gradxorr_nucl(ll,l)+gradlongkl
       enddo
       ehbcorr_nucl=ekont*ees
       return
       enddo
       ehbcorr_nucl=ekont*ees
       return
@@ -22511,9 +22137,9 @@
 !el local variables
       integer :: i,j,k,l,jj,kk,ll,ilist,m, iresshield
       real(kind=8) :: coeffp,coeffm,eij,ekl,ees0pij,ees0pkl,ees0mij,&
 !el local variables
       integer :: i,j,k,l,jj,kk,ll,ilist,m, iresshield
       real(kind=8) :: coeffp,coeffm,eij,ekl,ees0pij,ees0pkl,ees0mij,&
-                   ees0mkl,ees,coeffpees0pij,coeffmees0mij,&
-                   coeffpees0pkl,coeffmees0mkl,gradlongij,gradlongkl, &
-                   rlocshield
+               ees0mkl,ees,coeffpees0pij,coeffmees0mij,&
+               coeffpees0pkl,coeffmees0mkl,gradlongij,gradlongkl, &
+               rlocshield
 
       lprn=.false.
       eij=facont_hb(jj,i)
 
       lprn=.false.
       eij=facont_hb(jj,i)
@@ -22541,32 +22167,32 @@
       coeffpees0pkl=coeffp*ees0pkl
       coeffmees0mkl=coeffm*ees0mkl
       do ll=1,3
       coeffpees0pkl=coeffp*ees0pkl
       coeffmees0mkl=coeffm*ees0mkl
       do ll=1,3
-        gradxorr3_nucl(ll,i)=gradxorr3_nucl(ll,i) &
+      gradxorr3_nucl(ll,i)=gradxorr3_nucl(ll,i) &
        -ekont*(coeffpees0pkl*gacontp_hb1(ll,jj,i)+&
        coeffmees0mkl*gacontm_hb1(ll,jj,i))
        -ekont*(coeffpees0pkl*gacontp_hb1(ll,jj,i)+&
        coeffmees0mkl*gacontm_hb1(ll,jj,i))
-        gradxorr3_nucl(ll,j)=gradxorr3_nucl(ll,j) &
-        -ekont*(coeffpees0pkl*gacontp_hb2(ll,jj,i)+ &
-        coeffmees0mkl*gacontm_hb2(ll,jj,i))
-        gradxorr3_nucl(ll,k)=gradxorr3_nucl(ll,k) &
-        -ekont*(coeffpees0pij*gacontp_hb1(ll,kk,k)+ &
-        coeffmees0mij*gacontm_hb1(ll,kk,k))
-        gradxorr3_nucl(ll,l)=gradxorr3_nucl(ll,l) &
-        -ekont*(coeffpees0pij*gacontp_hb2(ll,kk,k)+ &
-        coeffmees0mij*gacontm_hb2(ll,kk,k))
-        gradlongij=ees*ekl*gacont_hbr(ll,jj,i)- &
-          ekont*(coeffpees0pkl*gacontp_hb3(ll,jj,i)+ &
-          coeffmees0mkl*gacontm_hb3(ll,jj,i))
-        gradcorr3_nucl(ll,j)=gradcorr3_nucl(ll,j)+gradlongij
-        gradcorr3_nucl(ll,i)=gradcorr3_nucl(ll,i)-gradlongij
-        gradlongkl=ees*eij*gacont_hbr(ll,kk,k)- &
-          ekont*(coeffpees0pij*gacontp_hb3(ll,kk,k)+ &
-          coeffmees0mij*gacontm_hb3(ll,kk,k))
-        gradcorr3_nucl(ll,l)=gradcorr3_nucl(ll,l)+gradlongkl
-        gradcorr3_nucl(ll,k)=gradcorr3_nucl(ll,k)-gradlongkl
-        gradxorr3_nucl(ll,i)=gradxorr3_nucl(ll,i)-gradlongij
-        gradxorr3_nucl(ll,j)=gradxorr3_nucl(ll,j)+gradlongij
-        gradxorr3_nucl(ll,k)=gradxorr3_nucl(ll,k)-gradlongkl
-        gradxorr3_nucl(ll,l)=gradxorr3_nucl(ll,l)+gradlongkl
+      gradxorr3_nucl(ll,j)=gradxorr3_nucl(ll,j) &
+      -ekont*(coeffpees0pkl*gacontp_hb2(ll,jj,i)+ &
+      coeffmees0mkl*gacontm_hb2(ll,jj,i))
+      gradxorr3_nucl(ll,k)=gradxorr3_nucl(ll,k) &
+      -ekont*(coeffpees0pij*gacontp_hb1(ll,kk,k)+ &
+      coeffmees0mij*gacontm_hb1(ll,kk,k))
+      gradxorr3_nucl(ll,l)=gradxorr3_nucl(ll,l) &
+      -ekont*(coeffpees0pij*gacontp_hb2(ll,kk,k)+ &
+      coeffmees0mij*gacontm_hb2(ll,kk,k))
+      gradlongij=ees*ekl*gacont_hbr(ll,jj,i)- &
+        ekont*(coeffpees0pkl*gacontp_hb3(ll,jj,i)+ &
+        coeffmees0mkl*gacontm_hb3(ll,jj,i))
+      gradcorr3_nucl(ll,j)=gradcorr3_nucl(ll,j)+gradlongij
+      gradcorr3_nucl(ll,i)=gradcorr3_nucl(ll,i)-gradlongij
+      gradlongkl=ees*eij*gacont_hbr(ll,kk,k)- &
+        ekont*(coeffpees0pij*gacontp_hb3(ll,kk,k)+ &
+        coeffmees0mij*gacontm_hb3(ll,kk,k))
+      gradcorr3_nucl(ll,l)=gradcorr3_nucl(ll,l)+gradlongkl
+      gradcorr3_nucl(ll,k)=gradcorr3_nucl(ll,k)-gradlongkl
+      gradxorr3_nucl(ll,i)=gradxorr3_nucl(ll,i)-gradlongij
+      gradxorr3_nucl(ll,j)=gradxorr3_nucl(ll,j)+gradlongij
+      gradxorr3_nucl(ll,k)=gradxorr3_nucl(ll,k)-gradlongkl
+      gradxorr3_nucl(ll,l)=gradxorr3_nucl(ll,l)+gradlongkl
       enddo
       ehbcorr3_nucl=ekont*ees
       return
       enddo
       ehbcorr3_nucl=ekont*ees
       return
@@ -22577,16 +22203,16 @@
       real(kind=8):: buffer(dimen1,dimen2)
       num_kont=num_cont_hb(atom)
       do i=1,num_kont
       real(kind=8):: buffer(dimen1,dimen2)
       num_kont=num_cont_hb(atom)
       do i=1,num_kont
-        do k=1,8
-          do j=1,3
-            buffer(i,indx+(k-1)*3+j)=zapas2(j,i,atom,k)
-          enddo ! j
-        enddo ! k
-        buffer(i,indx+25)=facont_hb(i,atom)
-        buffer(i,indx+26)=ees0p(i,atom)
-        buffer(i,indx+27)=ees0m(i,atom)
-        buffer(i,indx+28)=d_cont(i,atom)
-        buffer(i,indx+29)=dfloat(jcont_hb(i,atom))
+      do k=1,8
+        do j=1,3
+          buffer(i,indx+(k-1)*3+j)=zapas2(j,i,atom,k)
+        enddo ! j
+      enddo ! k
+      buffer(i,indx+25)=facont_hb(i,atom)
+      buffer(i,indx+26)=ees0p(i,atom)
+      buffer(i,indx+27)=ees0m(i,atom)
+      buffer(i,indx+28)=d_cont(i,atom)
+      buffer(i,indx+29)=dfloat(jcont_hb(i,atom))
       enddo ! i
       buffer(1,indx+30)=dfloat(num_kont)
       return
       enddo ! i
       buffer(1,indx+30)=dfloat(num_kont)
       return
@@ -22604,135 +22230,106 @@
       num_kont_old=num_cont_hb(atom)
       num_cont_hb(atom)=num_kont+num_kont_old
       do i=1,num_kont
       num_kont_old=num_cont_hb(atom)
       num_cont_hb(atom)=num_kont+num_kont_old
       do i=1,num_kont
-        ii=i+num_kont_old
-        do k=1,8
-          do j=1,3
-            zapas2(j,ii,atom,k)=buffer(i,indx+(k-1)*3+j)
-          enddo ! j 
-        enddo ! k 
-        facont_hb(ii,atom)=buffer(i,indx+25)
-        ees0p(ii,atom)=buffer(i,indx+26)
-        ees0m(ii,atom)=buffer(i,indx+27)
-        d_cont(i,atom)=buffer(i,indx+28)
-        jcont_hb(ii,atom)=buffer(i,indx+29)
+      ii=i+num_kont_old
+      do k=1,8
+        do j=1,3
+          zapas2(j,ii,atom,k)=buffer(i,indx+(k-1)*3+j)
+        enddo ! j 
+      enddo ! k 
+      facont_hb(ii,atom)=buffer(i,indx+25)
+      ees0p(ii,atom)=buffer(i,indx+26)
+      ees0m(ii,atom)=buffer(i,indx+27)
+      d_cont(i,atom)=buffer(i,indx+28)
+      jcont_hb(ii,atom)=buffer(i,indx+29)
       enddo ! i
       return
       end subroutine unpack_buffer
 !c------------------------------------------------------------------------------
 #endif
       subroutine ecatcat(ecationcation)
       enddo ! i
       return
       end subroutine unpack_buffer
 !c------------------------------------------------------------------------------
 #endif
       subroutine ecatcat(ecationcation)
-        integer :: i,j,itmp,xshift,yshift,zshift,subchap,k
-        real(kind=8) :: xi,yi,zi,xj,yj,zj,ract,rcat0,epscalc,r06,r012,&
-        r7,r4,ecationcation,k0,rcal
-        real(kind=8) xj_temp,yj_temp,zj_temp,xj_safe,yj_safe,zj_safe, &
-        dist_init,dist_temp,Evan1cat,Evan2cat,Eeleccat
-        real(kind=8),dimension(3) ::dEvan1Cmcat,dEvan2Cmcat,dEeleccat,&
-        gg,r
-
-        ecationcation=0.0d0
-        if (nres_molec(5).eq.0) return
-        rcat0=3.472
-        epscalc=0.05
-        r06 = rcat0**6
-        r012 = r06**2
-        k0 = 332.0*(2.0*2.0)/80.0
-        itmp=0
-        
-        do i=1,4
-        itmp=itmp+nres_molec(i)
-        enddo
+      integer :: i,j,itmp,xshift,yshift,zshift,subchap,k,itypi,itypj
+      real(kind=8) :: xi,yi,zi,xj,yj,zj,ract,rcat0,epscalc,r06,r012,&
+      r7,r4,ecationcation,k0,rcal,aa,bb,sslipi,ssgradlipi,sslipj,ssgradlipj
+      real(kind=8) xj_temp,yj_temp,zj_temp,xj_safe,yj_safe,zj_safe, &
+      dist_init,dist_temp,Evan1cat,Evan2cat,Eeleccat
+      real(kind=8),dimension(3) ::dEvan1Cmcat,dEvan2Cmcat,dEeleccat,&
+      gg,r
+
+      ecationcation=0.0d0
+      if (nres_molec(5).eq.0) return
+      rcat0=3.472
+      epscalc=0.05
+      r06 = rcat0**6
+      r012 = r06**2
+!        k0 = 332.0*(2.0*2.0)/80.0
+      itmp=0
+      
+      do i=1,4
+      itmp=itmp+nres_molec(i)
+      enddo
 !        write(iout,*) "itmp",itmp
 !        write(iout,*) "itmp",itmp
-        do i=itmp+1,itmp+nres_molec(5)-1
+      do i=itmp+1,itmp+nres_molec(5)-1
        
        
-        xi=c(1,i)
-        yi=c(2,i)
-        zi=c(3,i)
-         
-          xi=mod(xi,boxxsize)
-          if (xi.lt.0) xi=xi+boxxsize
-          yi=mod(yi,boxysize)
-          if (yi.lt.0) yi=yi+boxysize
-          zi=mod(zi,boxzsize)
-          if (zi.lt.0) zi=zi+boxzsize
-
-          do j=i+1,itmp+nres_molec(5)
+      xi=c(1,i)
+      yi=c(2,i)
+      zi=c(3,i)
+!        write (iout,*) i,"TUTUT",c(1,i)
+        itypi=itype(i,5)
+      call to_box(xi,yi,zi)
+      call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+        do j=i+1,itmp+nres_molec(5)
+        itypj=itype(j,5)
+!          print *,i,j,itypi,itypj
+        k0 = 332.0*(ichargecat(itypi)*ichargecat(itypj))/80.0
 !           print *,i,j,'catcat'
 !           print *,i,j,'catcat'
-           xj=c(1,j)
-           yj=c(2,j)
-           zj=c(3,j)
-          xj=dmod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=dmod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=dmod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
-!          write(iout,*) c(1,i),xi,xj,"xy",boxxsize
-      dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-      xj_safe=xj
-      yj_safe=yj
-      zj_safe=zj
-      subchap=0
-      do xshift=-1,1
-      do yshift=-1,1
-      do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-       enddo
-       enddo
-       enddo
-       if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-       else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-       endif
+         xj=c(1,j)
+         yj=c(2,j)
+         zj=c(3,j)
+      call to_box(xj,yj,zj)
+!      call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+!      aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+!       +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+!      bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+!       +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)
        rcal =xj**2+yj**2+zj**2
        rcal =xj**2+yj**2+zj**2
-        ract=sqrt(rcal)
+      ract=sqrt(rcal)
 !        rcat0=3.472
 !        epscalc=0.05
 !        r06 = rcat0**6
 !        r012 = r06**2
 !        k0 = 332*(2*2)/80
 !        rcat0=3.472
 !        epscalc=0.05
 !        r06 = rcat0**6
 !        r012 = r06**2
 !        k0 = 332*(2*2)/80
-        Evan1cat=epscalc*(r012/rcal**6)
-        Evan2cat=epscalc*2*(r06/rcal**3)
-        Eeleccat=k0/ract
-        r7 = rcal**7
-        r4 = rcal**4
-        r(1)=xj
-        r(2)=yj
-        r(3)=zj
-        do k=1,3
-          dEvan1Cmcat(k)=-12*r(k)*epscalc*r012/r7
-          dEvan2Cmcat(k)=-12*r(k)*epscalc*r06/r4
-          dEeleccat(k)=-k0*r(k)/ract**3
-        enddo
-        do k=1,3
-          gg(k) = dEvan1Cmcat(k)+dEvan2Cmcat(k)+dEeleccat(k)
-          gradcatcat(k,i)=gradcatcat(k,i)-gg(k)
-          gradcatcat(k,j)=gradcatcat(k,j)+gg(k)
-        enddo
-
+      Evan1cat=epscalc*(r012/(rcal**6))
+      Evan2cat=epscalc*2*(r06/(rcal**3))
+      Eeleccat=k0/ract
+      r7 = rcal**7
+      r4 = rcal**4
+      r(1)=xj
+      r(2)=yj
+      r(3)=zj
+      do k=1,3
+        dEvan1Cmcat(k)=-12*r(k)*epscalc*r012/r7
+        dEvan2Cmcat(k)=-12*r(k)*epscalc*r06/r4
+        dEeleccat(k)=-k0*r(k)/ract**3
+      enddo
+      do k=1,3
+        gg(k) = dEvan1Cmcat(k)+dEvan2Cmcat(k)+dEeleccat(k)
+        gradcatcat(k,i)=gradcatcat(k,i)-gg(k)
+        gradcatcat(k,j)=gradcatcat(k,j)+gg(k)
+      enddo
+      if (energy_dec) write (iout,*) i,j,Evan1cat,Evan2cat,Eeleccat,&
+       r012,rcal**6,ichargecat(itypi)*ichargecat(itypj)
 !        write(iout,*) "ecatcat",i,j, ecationcation,xj,yj,zj
 !        write(iout,*) "ecatcat",i,j, ecationcation,xj,yj,zj
-        ecationcation=ecationcation+Evan1cat+Evan2cat+Eeleccat
+      ecationcation=ecationcation+Evan1cat+Evan2cat+Eeleccat
        enddo
        enddo
        return 
        end subroutine ecatcat
 !---------------------------------------------------------------------------
 ! new for K+
        enddo
        enddo
        return 
        end subroutine ecatcat
 !---------------------------------------------------------------------------
 ! new for K+
-      subroutine ecats_prot_amber(ecations_prot_amber)
+      subroutine ecats_prot_amber(evdw)
 !      subroutine ecat_prot2(ecation_prot)
       use calc_data
       use comm_momo
 !      subroutine ecat_prot2(ecation_prot)
       use calc_data
       use comm_momo
@@ -22741,10 +22338,10 @@
 !el local variables
       integer :: iint,itypi1,subchap,isel,itmp
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,e1,e2,sigm,epsi
 !el local variables
       integer :: iint,itypi1,subchap,isel,itmp
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,e1,e2,sigm,epsi
-      real(kind=8) :: evdw
+      real(kind=8) :: evdw,aa,bb
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
-                    dist_temp, dist_init,ssgradlipi,ssgradlipj, &
-                    sslipi,sslipj,faclip,alpha_sco
+                dist_temp, dist_init,ssgradlipi,ssgradlipj, &
+                sslipi,sslipj,faclip,alpha_sco
       integer :: ii
       real(kind=8) :: fracinbuf
       real (kind=8) :: escpho
       integer :: ii
       real(kind=8) :: fracinbuf
       real (kind=8) :: escpho
@@ -22761,112 +22358,100 @@
       real(kind=8) ::  facd4, adler, Fgb, facd3
       integer troll,jj,istate
       real (kind=8) :: dcosom1(3),dcosom2(3)
       real(kind=8) ::  facd4, adler, Fgb, facd3
       integer troll,jj,istate
       real (kind=8) :: dcosom1(3),dcosom2(3)
+      real(kind=8) ::locbox(3)
+      locbox(1)=boxxsize
+          locbox(2)=boxysize
+      locbox(3)=boxzsize
 
 
-      ecations_prot_amber=0.0D0
+      evdw=0.0D0
       if (nres_molec(5).eq.0) return
       eps_out=80.0d0
 !      sss_ele_cut=1.0d0
 
       if (nres_molec(5).eq.0) return
       eps_out=80.0d0
 !      sss_ele_cut=1.0d0
 
-        itmp=0
-        do i=1,4
-        itmp=itmp+nres_molec(i)
-        enddo
+      itmp=0
+      do i=1,4
+      itmp=itmp+nres_molec(i)
+      enddo
+!        go to 17
 !        do i=1,nres_molec(1)-1  ! loop over all peptide groups needs parralelization
 !        do i=1,nres_molec(1)-1  ! loop over all peptide groups needs parralelization
-        do i=ibond_start,ibond_end
+      do i=ibond_start,ibond_end
 
 !        print *,"I am in EVDW",i
 
 !        print *,"I am in EVDW",i
-        itypi=iabs(itype(i,1))
+      itypi=iabs(itype(i,1))
+  
 !        if (i.ne.47) cycle
 !        if (i.ne.47) cycle
-        if (itypi.eq.ntyp1) cycle
-        itypi1=iabs(itype(i+1,1))
-        xi=c(1,nres+i)
-        yi=c(2,nres+i)
-        zi=c(3,nres+i)
-          xi=dmod(xi,boxxsize)
-          if (xi.lt.0) xi=xi+boxxsize
-          yi=dmod(yi,boxysize)
-          if (yi.lt.0) yi=yi+boxysize
-          zi=dmod(zi,boxzsize)
-          if (zi.lt.0) zi=zi+boxzsize
-        dxi=dc_norm(1,nres+i)
-        dyi=dc_norm(2,nres+i)
-        dzi=dc_norm(3,nres+i)
-        dsci_inv=vbld_inv(i+nres)
-         do j=itmp+1,itmp+nres_molec(5)
+      if ((itypi.eq.ntyp1).or.(itypi.eq.10)) cycle
+      itypi1=iabs(itype(i+1,1))
+      xi=c(1,nres+i)
+      yi=c(2,nres+i)
+      zi=c(3,nres+i)
+      call to_box(xi,yi,zi)
+      call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+      dxi=dc_norm(1,nres+i)
+      dyi=dc_norm(2,nres+i)
+      dzi=dc_norm(3,nres+i)
+      dsci_inv=vbld_inv(i+nres)
+       do j=itmp+1,itmp+nres_molec(5)
 
 ! Calculate SC interaction energy.
 
 ! Calculate SC interaction energy.
-            itypj=iabs(itype(j,1))
-            if ((itypj.eq.ntyp1)) cycle
-             CALL elgrad_init_cat(eheadtail,Egb,Ecl,Elj,Equad,Epol)
-
-            dscj_inv=vbld_inv(j+nres)
-           xj=c(1,j)
-           yj=c(2,j)
-           zj=c(3,j)
-           xj=dmod(xj,boxxsize)
-           if (xj.lt.0) xj=xj+boxxsize
-           yj=dmod(yj,boxysize)
-           if (yj.lt.0) yj=yj+boxysize
-           zj=dmod(zj,boxzsize)
-           if (zj.lt.0) zj=zj+boxzsize
-          dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          xj_safe=xj
-          yj_safe=yj
-          zj_safe=zj
-          subchap=0
-
-          do xshift=-1,1
-          do yshift=-1,1
-          do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-          enddo
-          enddo
-          enddo
-          if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-          else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-          endif
+          itypj=iabs(itype(j,5))
+          if ((itypj.eq.ntyp1)) cycle
+           CALL elgrad_init_cat(eheadtail,Egb,Ecl,Elj,Equad,Epol)
+
+          dscj_inv=0.0
+         xj=c(1,j)
+         yj=c(2,j)
+         zj=c(3,j)
+ 
+      call to_box(xj,yj,zj)
+!      write(iout,*) "xi,yi,zi,xj,yj,zj", xi,yi,zi,xj,yj,zj
+
+!      call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+!      aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+!       +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+!      bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+!       +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)
+!      write(iout,*) "xj,yj,zj", xj,yj,zj,boxxsize
 
 !          dxj = dc_norm( 1, nres+j )
 !          dyj = dc_norm( 2, nres+j )
 !          dzj = dc_norm( 3, nres+j )
 
 
 !          dxj = dc_norm( 1, nres+j )
 !          dyj = dc_norm( 2, nres+j )
 !          dzj = dc_norm( 3, nres+j )
 
-          itypi = itype(i,1)
-          itypj = itype(j,5)
+        itypi = itype(i,1)
+        itypj = itype(j,5)
 ! Parameters from fitting the analitical expressions to the PMF obtained by umbrella 
 ! sampling performed with amber package
 !          alf1   = 0.0d0
 !          alf2   = 0.0d0
 !          alf12  = 0.0d0
 !          a12sq = rborn(itypi,itypj) * rborn(itypj,itypi)
 ! Parameters from fitting the analitical expressions to the PMF obtained by umbrella 
 ! sampling performed with amber package
 !          alf1   = 0.0d0
 !          alf2   = 0.0d0
 !          alf12  = 0.0d0
 !          a12sq = rborn(itypi,itypj) * rborn(itypj,itypi)
-          chi1 = chicat(itypi,itypj)
-          chis1 = chiscat(itypi,itypj)
-          chip1 = chippcat(itypi,itypj)
+        chi1 = chi1cat(itypi,itypj)
+        chis1 = chis1cat(itypi,itypj)
+        chip1 = chipp1cat(itypi,itypj)
+!          chi1=0.0d0
+!          chis1=0.0d0
+!          chip1=0.0d0
+        chi2=0.0
+        chip2=0.0
+        chis2=0.0
 !          chis2 = chis(itypj,itypi)
 !          chis2 = chis(itypj,itypi)
-!          chis12 = chis1 * chis2
-          sig1 = sigmap1cat(itypi,itypj)
+        chis12 = chis1 * chis2
+        sig1 = sigmap1cat(itypi,itypj)
 !          sig2 = sigmap2(itypi,itypj)
 ! alpha factors from Fcav/Gcav
 !          sig2 = sigmap2(itypi,itypj)
 ! alpha factors from Fcav/Gcav
-          b1cav = alphasurcat(1,itypi,itypj)
-          b2cav = alphasurcat(2,itypi,itypj)
-          b3cav = alphasurcat(3,itypi,itypj)
-          b4cav = alphasurcat(4,itypi,itypj)
-          
+        b1cav = alphasurcat(1,itypi,itypj)
+        b2cav = alphasurcat(2,itypi,itypj)
+        b3cav = alphasurcat(3,itypi,itypj)
+        b4cav = alphasurcat(4,itypi,itypj)
+        
+!        b1cav=0.0d0
+!        b2cav=0.0d0
+!        b3cav=0.0d0
+!        b4cav=0.0d0
+ 
 ! used to determine whether we want to do quadrupole calculations
        eps_in = epsintabcat(itypi,itypj)
        if (eps_in.eq.0.0) eps_in=1.0
 ! used to determine whether we want to do quadrupole calculations
        eps_in = epsintabcat(itypi,itypj)
        if (eps_in.eq.0.0) eps_in=1.0
@@ -22875,18 +22460,20 @@
 !       Rtail = 0.0d0
 
        DO k = 1, 3
 !       Rtail = 0.0d0
 
        DO k = 1, 3
-        ctail(k,1)=c(k,i+nres)
-        ctail(k,2)=c(k,j)
+      ctail(k,1)=c(k,i+nres)
+      ctail(k,2)=c(k,j)
        END DO
        END DO
+      call to_box(ctail(1,1),ctail(2,1),ctail(3,1))
+      call to_box(ctail(1,2),ctail(2,2),ctail(3,2))
 !c! tail distances will be themselves usefull elswhere
 !c1 (in Gcav, for example)
 !c! tail distances will be themselves usefull elswhere
 !c1 (in Gcav, for example)
-       Rtail_distance(1) = ctail( 1, 2 ) - ctail( 1,1 )
-       Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 )
-       Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 )
+       do k=1,3
+       Rtail_distance(k) = boxshift(ctail(k,2) - ctail(k,1),locbox(k))
+       enddo 
        Rtail = dsqrt( &
        Rtail = dsqrt( &
-          (Rtail_distance(1)*Rtail_distance(1)) &
-        + (Rtail_distance(2)*Rtail_distance(2)) &
-        + (Rtail_distance(3)*Rtail_distance(3)))
+        (Rtail_distance(1)*Rtail_distance(1)) &
+      + (Rtail_distance(2)*Rtail_distance(2)) &
+      + (Rtail_distance(3)*Rtail_distance(3)))
 ! tail location and distance calculations
 ! dhead1
        d1 = dheadcat(1, 1, itypi, itypj)
 ! tail location and distance calculations
 ! dhead1
        d1 = dheadcat(1, 1, itypi, itypj)
@@ -22895,18 +22482,23 @@
 ! location of polar head is computed by taking hydrophobic centre
 ! and moving by a d1 * dc_norm vector
 ! see unres publications for very informative images
 ! location of polar head is computed by taking hydrophobic centre
 ! and moving by a d1 * dc_norm vector
 ! see unres publications for very informative images
-        chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
-        chead(k,2) = c(k, j)
+      chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
+      chead(k,2) = c(k, j)
+      enddo
+      call to_box(chead(1,1),chead(2,1),chead(3,1))
+      call to_box(chead(1,2),chead(2,2),chead(3,2))
+!      write(iout,*) "TEST",chead(1,1),chead(2,1),chead(3,1),dc_norm(k, i+nres),d1 
 ! distance 
 !        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
 ! distance 
 !        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
-!        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
-        Rhead_distance(k) = chead(k,2) - chead(k,1)
+!         Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
+      do k=1,3
+      Rhead_distance(k) = boxshift(chead(k,2) - chead(k,1),locbox(k))
        END DO
 ! pitagoras (root of sum of squares)
        Rhead = dsqrt( &
        END DO
 ! pitagoras (root of sum of squares)
        Rhead = dsqrt( &
-          (Rhead_distance(1)*Rhead_distance(1)) &
-        + (Rhead_distance(2)*Rhead_distance(2)) &
-        + (Rhead_distance(3)*Rhead_distance(3)))
+        (Rhead_distance(1)*Rhead_distance(1)) &
+      + (Rhead_distance(2)*Rhead_distance(2)) &
+      + (Rhead_distance(3)*Rhead_distance(3)))
 !-------------------------------------------------------------------
 ! zero everything that should be zero'ed
        evdwij = 0.0d0
 !-------------------------------------------------------------------
 ! zero everything that should be zero'ed
        evdwij = 0.0d0
@@ -22921,48 +22513,59 @@
        dGCLdOM12 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0
        dGCLdOM12 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0
-          Fcav = 0.0d0
-          dFdR = 0.0d0
-          dCAVdOM1  = 0.0d0
-          dCAVdOM2  = 0.0d0
-          dCAVdOM12 = 0.0d0
-          dscj_inv = vbld_inv(j+nres)
+        Fcav = 0.0d0
+        Fisocav=0.0d0
+        dFdR = 0.0d0
+        dCAVdOM1  = 0.0d0
+        dCAVdOM2  = 0.0d0
+        dCAVdOM12 = 0.0d0
+        dscj_inv = vbld_inv(j+nres)
 !          print *,i,j,dscj_inv,dsci_inv
 ! rij holds 1/(distance of Calpha atoms)
 !          print *,i,j,dscj_inv,dsci_inv
 ! rij holds 1/(distance of Calpha atoms)
-          rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
-          rij  = dsqrt(rrij)
-          CALL sc_angular
+        rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
+        rij  = dsqrt(rrij)
+        CALL sc_angular
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials
 ! om = omega, sqom = om^2
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials
 ! om = omega, sqom = om^2
-          sqom1  = om1 * om1
-          sqom2  = om2 * om2
-          sqom12 = om12 * om12
+        sqom1  = om1 * om1
+        sqom2  = om2 * om2
+        sqom12 = om12 * om12
 
 ! now we calculate EGB - Gey-Berne
 ! It will be summed up in evdwij and saved in evdw
 
 ! now we calculate EGB - Gey-Berne
 ! It will be summed up in evdwij and saved in evdw
-          sigsq     = 1.0D0  / sigsq
-          sig       = sig0ij * dsqrt(sigsq)
+        sigsq     = 1.0D0  / sigsq
+        sig       = sig0ij * dsqrt(sigsq)
 !          rij_shift = 1.0D0  / rij - sig + sig0ij
 !          rij_shift = 1.0D0  / rij - sig + sig0ij
-          rij_shift = Rtail - sig + sig0ij
-          IF (rij_shift.le.0.0D0) THEN
-           evdw = 1.0D20
-           RETURN
-          END IF
-          sigder = -sig * sigsq
-          rij_shift = 1.0D0 / rij_shift
-          fac       = rij_shift**expon
-          c1        = fac  * fac * aa_aq(itypi,itypj)
+        rij_shift = Rtail - sig + sig0ij
+        IF (rij_shift.le.0.0D0) THEN
+         evdw = 1.0D20
+      if (evdw.gt.1.0d6) then
+      write (*,'(2(1x,a3,i3),7f7.2)') &
+      restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
+      1.0d0/rij,Rtail,Rhead,rij_shift, sig, sig0ij,sigsq
+      write(*,*) facsig,faceps1_inv,om1,chiom1,chi1
+     write(*,*) "ANISO?!",chi1
+!evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
+!      Equad,evdwij+Fcav+eheadtail,evdw
+      endif
+
+         RETURN
+        END IF
+        sigder = -sig * sigsq
+        rij_shift = 1.0D0 / rij_shift
+        fac       = rij_shift**expon
+        c1        = fac  * fac * aa_aq_cat(itypi,itypj)
 !          print *,"ADAM",aa_aq(itypi,itypj)
 
 !          c1        = 0.0d0
 !          print *,"ADAM",aa_aq(itypi,itypj)
 
 !          c1        = 0.0d0
-          c2        = fac  * bb_aq(itypi,itypj)
+        c2        = fac  * bb_aq_cat(itypi,itypj)
 !          c2        = 0.0d0
 !          c2        = 0.0d0
-          evdwij    = eps1 * eps2rt * eps3rt * ( c1 + c2 )
-          eps2der   = eps3rt * evdwij
-          eps3der   = eps2rt * evdwij
+        evdwij    = eps1 * eps2rt * eps3rt * ( c1 + c2 )
+        eps2der   = eps3rt * evdwij
+        eps3der   = eps2rt * evdwij
 !          evdwij    = 4.0d0 * eps2rt * eps3rt * evdwij
 !          evdwij    = 4.0d0 * eps2rt * eps3rt * evdwij
-          evdwij    = eps2rt * eps3rt * evdwij
+        evdwij    = eps2rt * eps3rt * evdwij
 !#ifdef TSCSC
 !          IF (bb_aq(itypi,itypj).gt.0) THEN
 !           evdw_p = evdw_p + evdwij
 !#ifdef TSCSC
 !          IF (bb_aq(itypi,itypj).gt.0) THEN
 !           evdw_p = evdw_p + evdwij
@@ -22970,120 +22573,111 @@
 !           evdw_m = evdw_m + evdwij
 !          END IF
 !#else
 !           evdw_m = evdw_m + evdwij
 !          END IF
 !#else
-          evdw = evdw  &
-              + evdwij
+        evdw = evdw  &
+            + evdwij
 !#endif
 !#endif
-          c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
-          fac    = -expon * (c1 + evdwij) * rij_shift
-          sigder = fac * sigder
+        c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
+        fac    = -expon * (c1 + evdwij) * rij_shift
+        sigder = fac * sigder
 ! Calculate distance derivative
 ! Calculate distance derivative
-          gg(1) =  fac
-          gg(2) =  fac
-          gg(3) =  fac
-
-          fac = chis1 * sqom1 + chis2 * sqom2 &
-          - 2.0d0 * chis12 * om1 * om2 * om12
-          pom = 1.0d0 - chis1 * chis2 * sqom12
-          Lambf = (1.0d0 - (fac / pom))
-          Lambf = dsqrt(Lambf)
-          sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
-          Chif = Rtail * sparrow
-          ChiLambf = Chif * Lambf
-          eagle = dsqrt(ChiLambf)
-          bat = ChiLambf ** 11.0d0
-          top = b1cav * ( eagle + b2cav * ChiLambf - b3cav )
-          bot = 1.0d0 + b4cav * (ChiLambf ** 12.0d0)
-          botsq = bot * bot
-          Fcav = top / bot
+        gg(1) =  fac
+        gg(2) =  fac
+        gg(3) =  fac
+!       print *,"GG(1),distance grad",gg(1)
+        fac = chis1 * sqom1 + chis2 * sqom2 &
+        - 2.0d0 * chis12 * om1 * om2 * om12
+        pom = 1.0d0 - chis1 * chis2 * sqom12
+        Lambf = (1.0d0 - (fac / pom))
+        Lambf = dsqrt(Lambf)
+        sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
+        Chif = Rtail * sparrow
+        ChiLambf = Chif * Lambf
+        eagle = dsqrt(ChiLambf)
+        bat = ChiLambf ** 11.0d0
+        top = b1cav * ( eagle + b2cav * ChiLambf - b3cav )
+        bot = 1.0d0 + b4cav * (ChiLambf ** 12.0d0)
+        botsq = bot * bot
+        Fcav = top / bot
 
        dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
        dbot = 12.0d0 * b4cav * bat * Lambf
        dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
 
 
        dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
        dbot = 12.0d0 * b4cav * bat * Lambf
        dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
 
-          dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
-          dbot = 12.0d0 * b4cav * bat * Chif
-          eagle = Lambf * pom
-          dFdOM1  = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
-          dFdOM2  = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
-          dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
-              * (chis2 * om2 * om12 - om1) / (eagle * pom)
+        dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
+        dbot = 12.0d0 * b4cav * bat * Chif
+        eagle = Lambf * pom
+        dFdOM1  = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
+        dFdOM2  = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
+        dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
+            * (chis2 * om2 * om12 - om1) / (eagle * pom)
 
 
-          dFdL = ((dtop * bot - top * dbot) / botsq)
-          dCAVdOM1  = dFdL * ( dFdOM1 )
-          dCAVdOM2  = dFdL * ( dFdOM2 )
-          dCAVdOM12 = dFdL * ( dFdOM12 )
+        dFdL = ((dtop * bot - top * dbot) / botsq)
+        dCAVdOM1  = dFdL * ( dFdOM1 )
+        dCAVdOM2  = dFdL * ( dFdOM2 )
+        dCAVdOM12 = dFdL * ( dFdOM12 )
 
        DO k= 1, 3
 
        DO k= 1, 3
-        ertail(k) = Rtail_distance(k)/Rtail
+      ertail(k) = Rtail_distance(k)/Rtail
        END DO
        erdxi = scalar( ertail(1), dC_norm(1,i+nres) )
        erdxj = scalar( ertail(1), dC_norm(1,j) )
        END DO
        erdxi = scalar( ertail(1), dC_norm(1,i+nres) )
        erdxj = scalar( ertail(1), dC_norm(1,j) )
-       facd1 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
-       facd2 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
+       facd1 = dtailcat(1,itypi,itypj) * vbld_inv(i+nres)
+       facd2 = dtailcat(2,itypi,itypj) * vbld_inv(j)
        DO k = 1, 3
        DO k = 1, 3
-        pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
-        gvdwx(k,i) = gvdwx(k,i) &
-                  - (( dFdR + gg(k) ) * pom)
-        pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres))
+      pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
+      gradpepcatx(k,i) = gradpepcatx(k,i) &
+              - (( dFdR + gg(k) ) * pom)
+      pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j))
 !        gvdwx(k,j) = gvdwx(k,j)   &
 !                  + (( dFdR + gg(k) ) * pom)
 !        gvdwx(k,j) = gvdwx(k,j)   &
 !                  + (( dFdR + gg(k) ) * pom)
-        gvdwc(k,i) = gvdwc(k,i)  &
-                  - (( dFdR + gg(k) ) * ertail(k))
-        gvdwc(k,j) = gvdwc(k,j) &
-                  + (( dFdR + gg(k) ) * ertail(k))
-        gg(k) = 0.0d0
-
+      gradpepcat(k,i) = gradpepcat(k,i)  &
+              - (( dFdR + gg(k) ) * ertail(k))
+      gradpepcat(k,j) = gradpepcat(k,j) &
+              + (( dFdR + gg(k) ) * ertail(k))
+      gg(k) = 0.0d0
+       ENDDO
 !c! Compute head-head and head-tail energies for each state
 !c! Compute head-head and head-tail energies for each state
-          isel = iabs(Qi) + iabs(Qj)
-          IF (isel.eq.0) THEN
+!!        if (.false.) then ! turn off electrostatic
+        if (itype(j,5).gt.0) then ! the normal cation case
+        isel = iabs(Qi) + 1 ! ion is always charged so  iabs(Qj)
+!        print *,i,itype(i,1),isel
+        IF (isel.eq.0) THEN
 !c! No charges - do nothing
 !c! No charges - do nothing
-           eheadtail = 0.0d0
+         eheadtail = 0.0d0
 
 
-          ELSE IF (isel.eq.1 .and. iabs(Qj).eq.1) THEN
+        ELSE IF (isel.eq.1) THEN
 !c! Nonpolar-charge interactions
 !c! Nonpolar-charge interactions
-          if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
-            Qi=Qi*2
-            Qij=Qij*2
-           endif
-          if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
-            Qj=Qj*2
-            Qij=Qij*2
-           endif
+        if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
+          Qi=Qi*2
+          Qij=Qij*2
+         endif
 
 
-           CALL enq_cat(epol)
-           eheadtail = epol
+         CALL enq_cat(epol)
+         eheadtail = epol
 !           eheadtail = 0.0d0
 
 !           eheadtail = 0.0d0
 
-          ELSE IF (isel.eq.3 .and. icharge(itypj).eq.2) THEN
+        ELSE IF (isel.eq.3) THEN
 !c! Dipole-charge interactions
 !c! Dipole-charge interactions
-          if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
-            Qi=Qi*2
-            Qij=Qij*2
-           endif
-          if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
-            Qj=Qj*2
-            Qij=Qij*2
-           endif
-           CALL edq_cat(ecl, elj, epol)
-          eheadtail = ECL + elj + epol
+        if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
+          Qi=Qi*2
+          Qij=Qij*2
+         endif
+!         write(iout,*) "KURWA0",d1
+
+         CALL edq_cat(ecl, elj, epol)
+        eheadtail = ECL + elj + epol
 !           eheadtail = 0.0d0
 
 !           eheadtail = 0.0d0
 
-          ELSE IF ((isel.eq.2.and.   &
-               iabs(Qi).eq.1).and.  &
-               nstate(itypi,itypj).eq.1) THEN
+        ELSE IF ((isel.eq.2)) THEN
 
 !c! Same charge-charge interaction ( +/+ or -/- )
 
 !c! Same charge-charge interaction ( +/+ or -/- )
-          if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
-            Qi=Qi*2
-            Qij=Qij*2
-           endif
-          if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
-            Qj=Qj*2
-            Qij=Qij*2
-           endif
+        if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
+          Qi=Qi*2
+          Qij=Qij*2
+         endif
 
 
-           CALL eqq_cat(Ecl,Egb,Epol,Fisocav,Elj)
-           eheadtail = ECL + Egb + Epol + Fisocav + Elj
+         CALL eqq_cat(Ecl,Egb,Epol,Fisocav,Elj)
+         eheadtail = ECL + Egb + Epol + Fisocav + Elj
 !           eheadtail = 0.0d0
 
 !          ELSE IF ((isel.eq.2.and.  &
 !           eheadtail = 0.0d0
 
 !          ELSE IF ((isel.eq.2.and.  &
@@ -23101,25 +22695,336 @@
 !
 !           CALL energy_quad(istate,eheadtail,Ecl,Egb,Epol,Fisocav,Elj,Equad)
        END IF  ! this endif ends the "catch the gly-gly" at the beggining of Fcav
 !
 !           CALL energy_quad(istate,eheadtail,Ecl,Egb,Epol,Fisocav,Elj,Equad)
        END IF  ! this endif ends the "catch the gly-gly" at the beggining of Fcav
+       else
+       write(iout,*) "not yet implemented",j,itype(j,5)
+       endif
+!!       endif ! turn off electrostatic
       evdw = evdw  + Fcav + eheadtail
       evdw = evdw  + Fcav + eheadtail
+!      if (evdw.gt.1.0d6) then
+!      write (*,'(2(1x,a3,i3),3f6.2,10f16.7)') &
+!      restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
+!      1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
+!      Equad,evdwij+Fcav+eheadtail,evdw
+!      endif
 
        IF (energy_dec) write (iout,'(2(1x,a3,i3),3f6.2,10f16.7)') &
 
        IF (energy_dec) write (iout,'(2(1x,a3,i3),3f6.2,10f16.7)') &
-        restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
-        1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
-        Equad,evdwij+Fcav+eheadtail,evdw
+      restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
+      1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
+      Equad,evdwij+Fcav+eheadtail,evdw
+!       evdw = evdw  + Fcav  + eheadtail
+!       print *,"before sc_grad_cat", i,j, gradpepcat(1,j) 
+!        iF (nstate(itypi,itypj).eq.1) THEN
+      CALL sc_grad_cat
+!       print *,"after sc_grad_cat", i,j, gradpepcat(1,j)
+
+!       END IF
+!c!-------------------------------------------------------------------
+!c! NAPISY KONCOWE
+       END DO   ! j
+       END DO     ! i
+!c      write (iout,*) "Number of loop steps in EGB:",ind
+!c      energy_dec=.false.
+!              print *,"EVDW KURW",evdw,nres
+!!!        return
+   17   continue
+!      go to 23
+      do i=ibond_start,ibond_end
+
+!        print *,"I am in EVDW",i
+      itypi=10 ! the peptide group parameters are for glicine
+  
+!        if (i.ne.47) cycle
+      if ((itype(i,1).eq.ntyp1).or.itype(i+1,1).eq.ntyp1) cycle
+      itypi1=iabs(itype(i+1,1))
+      xi=(c(1,i)+c(1,i+1))/2.0
+      yi=(c(2,i)+c(2,i+1))/2.0
+      zi=(c(3,i)+c(3,i+1))/2.0
+        call to_box(xi,yi,zi)
+      dxi=dc_norm(1,i)
+      dyi=dc_norm(2,i)
+      dzi=dc_norm(3,i)
+      dsci_inv=vbld_inv(i+1)/2.0
+       do j=itmp+1,itmp+nres_molec(5)
+
+! Calculate SC interaction energy.
+          itypj=iabs(itype(j,5))
+          if ((itypj.eq.ntyp1)) cycle
+           CALL elgrad_init_cat_pep(eheadtail,Egb,Ecl,Elj,Equad,Epol)
+
+          dscj_inv=0.0
+         xj=c(1,j)
+         yj=c(2,j)
+         zj=c(3,j)
+        call to_box(xj,yj,zj)
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)
+
+        dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+
+        dxj = 0.0d0! dc_norm( 1, nres+j )
+        dyj = 0.0d0!dc_norm( 2, nres+j )
+        dzj = 0.0d0! dc_norm( 3, nres+j )
+
+        itypi = 10
+        itypj = itype(j,5)
+! Parameters from fitting the analitical expressions to the PMF obtained by umbrella 
+! sampling performed with amber package
+!          alf1   = 0.0d0
+!          alf2   = 0.0d0
+!          alf12  = 0.0d0
+!          a12sq = rborn(itypi,itypj) * rborn(itypj,itypi)
+        chi1 = chi1cat(itypi,itypj)
+        chis1 = chis1cat(itypi,itypj)
+        chip1 = chipp1cat(itypi,itypj)
+!          chi1=0.0d0
+!          chis1=0.0d0
+!          chip1=0.0d0
+        chi2=0.0
+        chip2=0.0
+        chis2=0.0
+!          chis2 = chis(itypj,itypi)
+        chis12 = chis1 * chis2
+        sig1 = sigmap1cat(itypi,itypj)
+!          sig2 = sigmap2(itypi,itypj)
+! alpha factors from Fcav/Gcav
+        b1cav = alphasurcat(1,itypi,itypj)
+        b2cav = alphasurcat(2,itypi,itypj)
+        b3cav = alphasurcat(3,itypi,itypj)
+        b4cav = alphasurcat(4,itypi,itypj)
+        
+! used to determine whether we want to do quadrupole calculations
+       eps_in = epsintabcat(itypi,itypj)
+       if (eps_in.eq.0.0) eps_in=1.0
+
+       eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out))
+!       Rtail = 0.0d0
+
+       DO k = 1, 3
+      ctail(k,1)=(c(k,i)+c(k,i+1))/2.0
+      ctail(k,2)=c(k,j)
+       END DO
+      call to_box(ctail(1,1),ctail(2,1),ctail(3,1))
+      call to_box(ctail(1,2),ctail(2,2),ctail(3,2))
+!c! tail distances will be themselves usefull elswhere
+!c1 (in Gcav, for example)
+       do k=1,3
+       Rtail_distance(k) = boxshift(ctail(k,2) - ctail(k,1),locbox(k))
+       enddo
+
+!c! tail distances will be themselves usefull elswhere
+!c1 (in Gcav, for example)
+       Rtail = dsqrt( &
+        (Rtail_distance(1)*Rtail_distance(1)) &
+      + (Rtail_distance(2)*Rtail_distance(2)) &
+      + (Rtail_distance(3)*Rtail_distance(3)))
+! tail location and distance calculations
+! dhead1
+       d1 = dheadcat(1, 1, itypi, itypj)
+!       print *,"d1",d1
+!       d1=0.0d0
+!       d2 = dhead(2, 1, itypi, itypj)
+       DO k = 1,3
+! location of polar head is computed by taking hydrophobic centre
+! and moving by a d1 * dc_norm vector
+! see unres publications for very informative images
+      chead(k,1) = (c(k, i)+c(k,i+1))/2.0 + d1 * dc_norm(k, i)
+      chead(k,2) = c(k, j)
+       ENDDO
+! distance 
+!        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
+!        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
+      call to_box(chead(1,1),chead(2,1),chead(3,1))
+      call to_box(chead(1,2),chead(2,2),chead(3,2))
+
+! distance 
+!        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
+!         Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
+      do k=1,3
+      Rhead_distance(k) = boxshift(chead(k,2) - chead(k,1),locbox(k))
+       END DO
+
+! pitagoras (root of sum of squares)
+       Rhead = dsqrt( &
+        (Rhead_distance(1)*Rhead_distance(1)) &
+      + (Rhead_distance(2)*Rhead_distance(2)) &
+      + (Rhead_distance(3)*Rhead_distance(3)))
+!-------------------------------------------------------------------
+! zero everything that should be zero'ed
+       evdwij = 0.0d0
+       ECL = 0.0d0
+       Elj = 0.0d0
+       Equad = 0.0d0
+       Epol = 0.0d0
+       Fcav=0.0d0
+       eheadtail = 0.0d0
+       dGCLdOM1 = 0.0d0
+       dGCLdOM2 = 0.0d0
+       dGCLdOM12 = 0.0d0
+       dPOLdOM1 = 0.0d0
+       dPOLdOM2 = 0.0d0
+        Fcav = 0.0d0
+        dFdR = 0.0d0
+        dCAVdOM1  = 0.0d0
+        dCAVdOM2  = 0.0d0
+        dCAVdOM12 = 0.0d0
+        dscj_inv = vbld_inv(j+nres)
+!          print *,i,j,dscj_inv,dsci_inv
+! rij holds 1/(distance of Calpha atoms)
+        rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
+        rij  = dsqrt(rrij)
+        CALL sc_angular
+! this should be in elgrad_init but om's are calculated by sc_angular
+! which in turn is used by older potentials
+! om = omega, sqom = om^2
+        sqom1  = om1 * om1
+        sqom2  = om2 * om2
+        sqom12 = om12 * om12
+
+! now we calculate EGB - Gey-Berne
+! It will be summed up in evdwij and saved in evdw
+        sigsq     = 1.0D0  / sigsq
+        sig       = sig0ij * dsqrt(sigsq)
+!          rij_shift = 1.0D0  / rij - sig + sig0ij
+        rij_shift = Rtail - sig + sig0ij
+        IF (rij_shift.le.0.0D0) THEN
+         evdw = 1.0D20
+!      if (evdw.gt.1.0d6) then
+!      write (*,'(2(1x,a3,i3),6f6.2)') &
+!      restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
+!      1.0d0/rij,Rtail,Rhead,rij_shift, sig, sig0ij
+!evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
+!      Equad,evdwij+Fcav+eheadtail,evdw
+!      endif
+         RETURN
+        END IF
+        sigder = -sig * sigsq
+        rij_shift = 1.0D0 / rij_shift
+        fac       = rij_shift**expon
+        c1        = fac  * fac * aa_aq_cat(itypi,itypj)
+!          print *,"ADAM",aa_aq(itypi,itypj)
+
+!          c1        = 0.0d0
+        c2        = fac  * bb_aq_cat(itypi,itypj)
+!          c2        = 0.0d0
+        evdwij    = eps1 * eps2rt * eps3rt * ( c1 + c2 )
+        eps2der   = eps3rt * evdwij
+        eps3der   = eps2rt * evdwij
+!          evdwij    = 4.0d0 * eps2rt * eps3rt * evdwij
+        evdwij    = eps2rt * eps3rt * evdwij
+!#ifdef TSCSC
+!          IF (bb_aq(itypi,itypj).gt.0) THEN
+!           evdw_p = evdw_p + evdwij
+!          ELSE
+!           evdw_m = evdw_m + evdwij
+!          END IF
+!#else
+        evdw = evdw  &
+            + evdwij
+!#endif
+        c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
+        fac    = -expon * (c1 + evdwij) * rij_shift
+        sigder = fac * sigder
+! Calculate distance derivative
+        gg(1) =  fac
+        gg(2) =  fac
+        gg(3) =  fac
+
+        fac = chis1 * sqom1 + chis2 * sqom2 &
+        - 2.0d0 * chis12 * om1 * om2 * om12
+        
+        pom = 1.0d0 - chis1 * chis2 * sqom12
+!          print *,"TUT2",fac,chis1,sqom1,pom
+        Lambf = (1.0d0 - (fac / pom))
+        Lambf = dsqrt(Lambf)
+        sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
+        Chif = Rtail * sparrow
+        ChiLambf = Chif * Lambf
+        eagle = dsqrt(ChiLambf)
+        bat = ChiLambf ** 11.0d0
+        top = b1cav * ( eagle + b2cav * ChiLambf - b3cav )
+        bot = 1.0d0 + b4cav * (ChiLambf ** 12.0d0)
+        botsq = bot * bot
+        Fcav = top / bot
+
+       dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
+       dbot = 12.0d0 * b4cav * bat * Lambf
+       dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
+
+        dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
+        dbot = 12.0d0 * b4cav * bat * Chif
+        eagle = Lambf * pom
+        dFdOM1  = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
+        dFdOM2  = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
+        dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
+            * (chis2 * om2 * om12 - om1) / (eagle * pom)
+
+        dFdL = ((dtop * bot - top * dbot) / botsq)
+        dCAVdOM1  = dFdL * ( dFdOM1 )
+        dCAVdOM2  = dFdL * ( dFdOM2 )
+        dCAVdOM12 = dFdL * ( dFdOM12 )
+
+       DO k= 1, 3
+      ertail(k) = Rtail_distance(k)/Rtail
+       END DO
+       erdxi = scalar( ertail(1), dC_norm(1,i) )
+       erdxj = scalar( ertail(1), dC_norm(1,j) )
+       facd1 = dtailcat(1,itypi,itypj) * vbld_inv(i)
+       facd2 = dtailcat(2,itypi,itypj) * vbld_inv(j+nres)
+       DO k = 1, 3
+      pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i))
+!        gradpepcatx(k,i) = gradpepcatx(k,i) &
+!                  - (( dFdR + gg(k) ) * pom)
+      pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres))
+!        gvdwx(k,j) = gvdwx(k,j)   &
+!                  + (( dFdR + gg(k) ) * pom)
+      gradpepcat(k,i) = gradpepcat(k,i)  &
+              - (( dFdR + gg(k) ) * ertail(k))/2.0d0
+      gradpepcat(k,i+1) = gradpepcat(k,i+1)  &
+              - (( dFdR + gg(k) ) * ertail(k))/2.0d0
+
+      gradpepcat(k,j) = gradpepcat(k,j) &
+              + (( dFdR + gg(k) ) * ertail(k))
+      gg(k) = 0.0d0
+       ENDDO
+      if (itype(j,5).gt.0) then
+!c! Compute head-head and head-tail energies for each state
+        isel = 3
+!c! Dipole-charge interactions
+         CALL edq_cat_pep(ecl, elj, epol)
+         eheadtail = ECL + elj + epol
+!          print *,"i,",i,eheadtail
+!           eheadtail = 0.0d0
+      else
+!HERE WATER and other types of molecules solvents will be added
+      write(iout,*) "not yet implemented"
+!      CALL edd_cat_pep
+      endif
+      evdw = evdw  + Fcav + eheadtail
+!      if (evdw.gt.1.0d6) then
+!      write (*,'(2(1x,a3,i3),3f6.2,10f16.7)') &
+!      restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
+!      1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
+!      Equad,evdwij+Fcav+eheadtail,evdw
+!      endif
+       IF (energy_dec) write (iout,'(2(1x,a3,i3),3f6.2,10f16.7)') &
+      restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
+      1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
+      Equad,evdwij+Fcav+eheadtail,evdw
 !       evdw = evdw  + Fcav  + eheadtail
 
 !        iF (nstate(itypi,itypj).eq.1) THEN
 !       evdw = evdw  + Fcav  + eheadtail
 
 !        iF (nstate(itypi,itypj).eq.1) THEN
-        CALL sc_grad_cat
+      CALL sc_grad_cat_pep
 !       END IF
 !c!-------------------------------------------------------------------
 !c! NAPISY KONCOWE
 !       END IF
 !c!-------------------------------------------------------------------
 !c! NAPISY KONCOWE
-         END DO   ! j
-        END DO    ! iint
+       END DO   ! j
        END DO     ! i
 !c      write (iout,*) "Number of loop steps in EGB:",ind
 !c      energy_dec=.false.
 !              print *,"EVDW KURW",evdw,nres
        END DO     ! i
 !c      write (iout,*) "Number of loop steps in EGB:",ind
 !c      energy_dec=.false.
 !              print *,"EVDW KURW",evdw,nres
+ 23   continue
+!       print *,"before leave sc_grad_cat", i,j, gradpepcat(1,nres-1)
 
       return
       end subroutine ecats_prot_amber
 
       return
       end subroutine ecats_prot_amber
@@ -23130,109 +23035,69 @@
 !      use calc_data
 !      use comm_momo
        integer i,j,k,subchap,itmp,inum
 !      use calc_data
 !      use comm_momo
        integer i,j,k,subchap,itmp,inum
-        real(kind=8) :: xi,yi,zi,xj,yj,zj,ract,rcat0,epscalc,r06,r012,&
-        r7,r4,ecationcation
-        real(kind=8) xj_temp,yj_temp,zj_temp,xj_safe,yj_safe,zj_safe, &
-        dist_init,dist_temp,ecation_prot,rcal,rocal,   &
-        Evan1,Evan2,EC,cm1mag,DASGL,delta,r0p,Epepcat, &
-        catl,cml,calpl, Etotal_p, Etotal_m,rtab,wdip,wmodquad,wquad1, &
-        wquad2,wvan1,E1,E2,wconst,wvan2,rcpm,dcmag,sin2thet,sinthet,  &
-        costhet,v1m,v2m,wh2o,wc,rsecp,Ir,Irsecp,Irthrp,Irfourp,Irfiftp,&
-        Irsistp,Irseven,Irtwelv,Irthir,dE1dr,dE2dr,dEdcos,wquad2p,opt, &
-        rs,rthrp,rfourp,rsixp,reight,Irsixp,Ireight,Irtw,Irfourt,      &
-        opt1,opt2,opt3,opt4,opt5,opt6,opt7,opt8,opt9,opt10,opt11,opt12,&
-        opt13,opt14,opt15,opt16,opt17,opt18,opt19, &
-        Equad1,Equad2,dscmag,v1dpv2,dscmag3,constA,constB,Edip,&
-        ndiv,ndivi
-        real(kind=8),dimension(3) ::dEvan1Cmcat,dEvan2Cmcat,dEeleccat,&
-        gg,r,EtotalCat,dEtotalCm,dEtotalCalp,dEvan1Cm,dEvan2Cm, &
-        dEtotalpep,dEtotalcat_num,dEddci,dEtotalcm_num,dEtotalcalp_num, &
-        tab1,tab2,tab3,diff,cm1,sc,p,tcat,talp,cm,drcp,drcp_norm,vcat,  &
-        v1,v2,v3,myd_norm,dx,vcm,valpha,drdpep,dcosdpep,dcosddci,dEdpep,&
-        dEcCat,dEdipCm,dEdipCalp,dEquad1Cat,dEquad1Cm,dEquad1Calp,      &
-        dEquad2Cat,dEquad2Cm,dEquad2Calpd,Evan1Cat,dEvan1Calp,dEvan2Cat,&
-        dEvan2Calp,dEtotalCat,dscvec,dEcCm,dEcCalp,dEdipCat,dEquad2Calp,&
-        dEvan1Cat
-        real(kind=8),dimension(6) :: vcatprm
-        ecation_prot=0.0d0
+      real(kind=8) :: xi,yi,zi,xj,yj,zj,ract,rcat0,epscalc,r06,r012,&
+      r7,r4,ecationcation
+      real(kind=8) xj_temp,yj_temp,zj_temp,xj_safe,yj_safe,zj_safe, &
+      dist_init,dist_temp,ecation_prot,rcal,rocal,   &
+      Evan1,Evan2,EC,cm1mag,DASGL,delta,r0p,Epepcat, &
+      catl,cml,calpl, Etotal_p, Etotal_m,rtab,wdip,wmodquad,wquad1, &
+      wquad2,wvan1,E1,E2,wconst,wvan2,rcpm,dcmag,sin2thet,sinthet,  &
+      costhet,v1m,v2m,wh2o,wc,rsecp,Ir,Irsecp,Irthrp,Irfourp,Irfiftp,&
+      Irsistp,Irseven,Irtwelv,Irthir,dE1dr,dE2dr,dEdcos,wquad2p,opt, &
+      rs,rthrp,rfourp,rsixp,reight,Irsixp,Ireight,Irtw,Irfourt,      &
+      opt1,opt2,opt3,opt4,opt5,opt6,opt7,opt8,opt9,opt10,opt11,opt12,&
+      opt13,opt14,opt15,opt16,opt17,opt18,opt19, &
+      Equad1,Equad2,dscmag,v1dpv2,dscmag3,constA,constB,Edip,&
+      ndiv,ndivi
+      real(kind=8),dimension(3) ::dEvan1Cmcat,dEvan2Cmcat,dEeleccat,&
+      gg,r,EtotalCat,dEtotalCm,dEtotalCalp,dEvan1Cm,dEvan2Cm, &
+      dEtotalpep,dEtotalcat_num,dEddci,dEtotalcm_num,dEtotalcalp_num, &
+      tab1,tab2,tab3,diff,cm1,sc,p,tcat,talp,cm,drcp,drcp_norm,vcat,  &
+      v1,v2,v3,myd_norm,dx,vcm,valpha,drdpep,dcosdpep,dcosddci,dEdpep,&
+      dEcCat,dEdipCm,dEdipCalp,dEquad1Cat,dEquad1Cm,dEquad1Calp,      &
+      dEquad2Cat,dEquad2Cm,dEquad2Calpd,Evan1Cat,dEvan1Calp,dEvan2Cat,&
+      dEvan2Calp,dEtotalCat,dscvec,dEcCm,dEcCalp,dEdipCat,dEquad2Calp,&
+      dEvan1Cat
+      real(kind=8),dimension(6) :: vcatprm
+      ecation_prot=0.0d0
 ! first lets calculate interaction with peptide groups
 ! first lets calculate interaction with peptide groups
-        if (nres_molec(5).eq.0) return
-        itmp=0
-        do i=1,4
-        itmp=itmp+nres_molec(i)
-        enddo
+      if (nres_molec(5).eq.0) return
+      itmp=0
+      do i=1,4
+      itmp=itmp+nres_molec(i)
+      enddo
 !        do i=1,nres_molec(1)-1  ! loop over all peptide groups needs parralelization
 !        do i=1,nres_molec(1)-1  ! loop over all peptide groups needs parralelization
-        do i=ibond_start,ibond_end
+      do i=ibond_start,ibond_end
 !         cycle
 !         cycle
-         if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1)) cycle ! leave dummy atoms
-        xi=0.5d0*(c(1,i)+c(1,i+1))
-        yi=0.5d0*(c(2,i)+c(2,i+1))
-        zi=0.5d0*(c(3,i)+c(3,i+1))
-          xi=mod(xi,boxxsize)
-          if (xi.lt.0) xi=xi+boxxsize
-          yi=mod(yi,boxysize)
-          if (yi.lt.0) yi=yi+boxysize
-          zi=mod(zi,boxzsize)
-          if (zi.lt.0) zi=zi+boxzsize
-
-         do j=itmp+1,itmp+nres_molec(5)
+       if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1)) cycle ! leave dummy atoms
+      xi=0.5d0*(c(1,i)+c(1,i+1))
+      yi=0.5d0*(c(2,i)+c(2,i+1))
+      zi=0.5d0*(c(3,i)+c(3,i+1))
+        call to_box(xi,yi,zi)
+
+       do j=itmp+1,itmp+nres_molec(5)
 !           print *,"WTF",itmp,j,i
 ! all parameters were for Ca2+ to approximate single charge divide by two
 !           print *,"WTF",itmp,j,i
 ! all parameters were for Ca2+ to approximate single charge divide by two
-         ndiv=1.0
-         if ((itype(j,5).eq.1).or.(itype(j,5).eq.3)) ndiv=2.0
-         wconst=78*ndiv
-        wdip =1.092777950857032D2
-        wdip=wdip/wconst
-        wmodquad=-2.174122713004870D4
-        wmodquad=wmodquad/wconst
-        wquad1 = 3.901232068562804D1
-        wquad1=wquad1/wconst
-        wquad2 = 3
-        wquad2=wquad2/wconst
-        wvan1 = 0.1
-        wvan2 = 6
+       ndiv=1.0
+       if ((itype(j,5).eq.1).or.(itype(j,5).eq.3)) ndiv=2.0
+       wconst=78*ndiv
+      wdip =1.092777950857032D2
+      wdip=wdip/wconst
+      wmodquad=-2.174122713004870D4
+      wmodquad=wmodquad/wconst
+      wquad1 = 3.901232068562804D1
+      wquad1=wquad1/wconst
+      wquad2 = 3
+      wquad2=wquad2/wconst
+      wvan1 = 0.1
+      wvan2 = 6
 !        itmp=0
 
 !        itmp=0
 
-           xj=c(1,j)
-           yj=c(2,j)
-           zj=c(3,j)
-          xj=dmod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=dmod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=dmod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
+         xj=c(1,j)
+         yj=c(2,j)
+         zj=c(3,j)
+        call to_box(xj,yj,zj)
       dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
       dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-      xj_safe=xj
-      yj_safe=yj
-      zj_safe=zj
-      subchap=0
-      do xshift=-1,1
-      do yshift=-1,1
-      do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-       enddo
-       enddo
-       enddo
-       if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-       else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-       endif
 !       enddo
 !       enddo
        rcpm = sqrt(xj**2+yj**2+zj**2)
 !       enddo
 !       enddo
        rcpm = sqrt(xj**2+yj**2+zj**2)
@@ -23245,498 +23110,675 @@
        enddo
        dcmag=dsqrt(dcmag)
        do k=1,3
        enddo
        dcmag=dsqrt(dcmag)
        do k=1,3
-         myd_norm(k)=dc(k,i)/dcmag
+       myd_norm(k)=dc(k,i)/dcmag
        enddo
        enddo
-        costhet=drcp_norm(1)*myd_norm(1)+drcp_norm(2)*myd_norm(2)+&
-        drcp_norm(3)*myd_norm(3)
-        rsecp = rcpm**2
-        Ir = 1.0d0/rcpm
-        Irsecp = 1.0d0/rsecp
-        Irthrp = Irsecp/rcpm
-        Irfourp = Irthrp/rcpm
-        Irfiftp = Irfourp/rcpm
-        Irsistp=Irfiftp/rcpm
-        Irseven=Irsistp/rcpm
-        Irtwelv=Irsistp*Irsistp
-        Irthir=Irtwelv/rcpm
-        sin2thet = (1-costhet*costhet)
-        sinthet=sqrt(sin2thet)
-        E1 = wdip*Irsecp*costhet+(wmodquad*Irfourp+wquad1*Irthrp)&
-             *sin2thet
-        E2 = -wquad1*Irthrp*wquad2+wvan1*(wvan2**12*Irtwelv-&
-             2*wvan2**6*Irsistp)
-        ecation_prot = ecation_prot+E1+E2
+      costhet=drcp_norm(1)*myd_norm(1)+drcp_norm(2)*myd_norm(2)+&
+      drcp_norm(3)*myd_norm(3)
+      rsecp = rcpm**2
+      Ir = 1.0d0/rcpm
+      Irsecp = 1.0d0/rsecp
+      Irthrp = Irsecp/rcpm
+      Irfourp = Irthrp/rcpm
+      Irfiftp = Irfourp/rcpm
+      Irsistp=Irfiftp/rcpm
+      Irseven=Irsistp/rcpm
+      Irtwelv=Irsistp*Irsistp
+      Irthir=Irtwelv/rcpm
+      sin2thet = (1-costhet*costhet)
+      sinthet=sqrt(sin2thet)
+      E1 = wdip*Irsecp*costhet+(wmodquad*Irfourp+wquad1*Irthrp)&
+           *sin2thet
+      E2 = -wquad1*Irthrp*wquad2+wvan1*(wvan2**12*Irtwelv-&
+           2*wvan2**6*Irsistp)
+      ecation_prot = ecation_prot+E1+E2
 !        print *,"ecatprot",i,j,ecation_prot,rcpm
 !        print *,"ecatprot",i,j,ecation_prot,rcpm
-        dE1dr = -2*costhet*wdip*Irthrp-& 
-         (4*wmodquad*Irfiftp+3*wquad1*Irfourp)*sin2thet
-        dE2dr = 3*wquad1*wquad2*Irfourp-     &
-          12*wvan1*wvan2**6*(wvan2**6*Irthir-Irseven)
-        dEdcos = wdip*Irsecp-2*(wmodquad*Irfourp+wquad1*Irthrp)*costhet
-        do k=1,3
-          drdpep(k) = -drcp_norm(k)
-          dcosdpep(k) = Ir*(costhet*drcp_norm(k)-myd_norm(k))
-          dcosddci(k) = drcp_norm(k)/dcmag-costhet*myd_norm(k)/dcmag
-          dEdpep(k) = (dE1dr+dE2dr)*drdpep(k)+dEdcos*dcosdpep(k)
-          dEddci(k) = dEdcos*dcosddci(k)
-        enddo
-        do k=1,3
-        gradpepcat(k,i)=gradpepcat(k,i)+0.5D0*dEdpep(k)-dEddci(k)
-        gradpepcat(k,i+1)=gradpepcat(k,i+1)+0.5D0*dEdpep(k)+dEddci(k)
-        gradpepcat(k,j)=gradpepcat(k,j)-dEdpep(k)
-        enddo
+      dE1dr = -2*costhet*wdip*Irthrp-& 
+       (4*wmodquad*Irfiftp+3*wquad1*Irfourp)*sin2thet
+      dE2dr = 3*wquad1*wquad2*Irfourp-     &
+        12*wvan1*wvan2**6*(wvan2**6*Irthir-Irseven)
+      dEdcos = wdip*Irsecp-2*(wmodquad*Irfourp+wquad1*Irthrp)*costhet
+      do k=1,3
+        drdpep(k) = -drcp_norm(k)
+        dcosdpep(k) = Ir*(costhet*drcp_norm(k)-myd_norm(k))
+        dcosddci(k) = drcp_norm(k)/dcmag-costhet*myd_norm(k)/dcmag
+        dEdpep(k) = (dE1dr+dE2dr)*drdpep(k)+dEdcos*dcosdpep(k)
+        dEddci(k) = dEdcos*dcosddci(k)
+      enddo
+      do k=1,3
+      gradpepcat(k,i)=gradpepcat(k,i)+0.5D0*dEdpep(k)-dEddci(k)
+      gradpepcat(k,i+1)=gradpepcat(k,i+1)+0.5D0*dEdpep(k)+dEddci(k)
+      gradpepcat(k,j)=gradpepcat(k,j)-dEdpep(k)
+      enddo
        enddo ! j
        enddo ! i
 !------------------------------------------sidechains
 !        do i=1,nres_molec(1)
        enddo ! j
        enddo ! i
 !------------------------------------------sidechains
 !        do i=1,nres_molec(1)
-        do i=ibond_start,ibond_end
-         if ((itype(i,1).eq.ntyp1)) cycle ! leave dummy atoms
+      do i=ibond_start,ibond_end
+       if ((itype(i,1).eq.ntyp1)) cycle ! leave dummy atoms
 !         cycle
 !        print *,i,ecation_prot
 !         cycle
 !        print *,i,ecation_prot
-        xi=(c(1,i+nres))
-        yi=(c(2,i+nres))
-        zi=(c(3,i+nres))
-          xi=mod(xi,boxxsize)
-          if (xi.lt.0) xi=xi+boxxsize
-          yi=mod(yi,boxysize)
-          if (yi.lt.0) yi=yi+boxysize
-          zi=mod(zi,boxzsize)
-          if (zi.lt.0) zi=zi+boxzsize
-          do k=1,3
-            cm1(k)=dc(k,i+nres)
-          enddo
-           cm1mag=sqrt(cm1(1)**2+cm1(2)**2+cm1(3)**2)
-         do j=itmp+1,itmp+nres_molec(5)
-         ndiv=1.0
-         if ((itype(j,5).eq.1).or.(itype(j,5).eq.3)) ndiv=2.0
-
-           xj=c(1,j)
-           yj=c(2,j)
-           zj=c(3,j)
-          xj=dmod(xj,boxxsize)
-          if (xj.lt.0) xj=xj+boxxsize
-          yj=dmod(yj,boxysize)
-          if (yj.lt.0) yj=yj+boxysize
-          zj=dmod(zj,boxzsize)
-          if (zj.lt.0) zj=zj+boxzsize
+      xi=(c(1,i+nres))
+      yi=(c(2,i+nres))
+      zi=(c(3,i+nres))
+                call to_box(xi,yi,zi)
+        do k=1,3
+          cm1(k)=dc(k,i+nres)
+        enddo
+         cm1mag=sqrt(cm1(1)**2+cm1(2)**2+cm1(3)**2)
+       do j=itmp+1,itmp+nres_molec(5)
+       ndiv=1.0
+       if ((itype(j,5).eq.1).or.(itype(j,5).eq.3)) ndiv=2.0
+
+         xj=c(1,j)
+         yj=c(2,j)
+         zj=c(3,j)
+        call to_box(xj,yj,zj)
       dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
       dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-      xj_safe=xj
-      yj_safe=yj
-      zj_safe=zj
-      subchap=0
-      do xshift=-1,1
-      do yshift=-1,1
-      do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-       enddo
-       enddo
-       enddo
-       if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-       else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-       endif
 !       enddo
 !       enddo
 ! 15- Glu 16-Asp
 !       enddo
 !       enddo
 ! 15- Glu 16-Asp
-         if((itype(i,1).eq.15.or.itype(i,1).eq.16).or.&
-         ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.&
-         (itype(i,1).eq.25))) then
-            if(itype(i,1).eq.16) then
-            inum=1
-            else
-            inum=2
-            endif
-            do k=1,6
-            vcatprm(k)=catprm(k,inum)
-            enddo
-            dASGL=catprm(7,inum)
+       if((itype(i,1).eq.15.or.itype(i,1).eq.16).or.&
+       ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.&
+       (itype(i,1).eq.25))) then
+          if(itype(i,1).eq.16) then
+          inum=1
+          else
+          inum=2
+          endif
+          do k=1,6
+          vcatprm(k)=catprm(k,inum)
+          enddo
+          dASGL=catprm(7,inum)
 !             do k=1,3
 !                vcm(k)=(cm1(k)/cm1mag)*dASGL+c(k,i+nres)
 !             do k=1,3
 !                vcm(k)=(cm1(k)/cm1mag)*dASGL+c(k,i+nres)
-                vcm(1)=(cm1(1)/cm1mag)*dASGL+xi
-                vcm(2)=(cm1(2)/cm1mag)*dASGL+yi
-                vcm(3)=(cm1(3)/cm1mag)*dASGL+zi
+            vcm(1)=(cm1(1)/cm1mag)*dASGL+xi
+            vcm(2)=(cm1(2)/cm1mag)*dASGL+yi
+            vcm(3)=(cm1(3)/cm1mag)*dASGL+zi
 
 !                valpha(k)=c(k,i)
 !                vcat(k)=c(k,j)
 
 !                valpha(k)=c(k,i)
 !                vcat(k)=c(k,j)
-                if (subchap.eq.1) then
-                 vcat(1)=xj_temp
-                 vcat(2)=yj_temp
-                 vcat(3)=zj_temp
-                 else
-                vcat(1)=xj_safe
-                vcat(2)=yj_safe
-                vcat(3)=zj_safe
-                 endif
-                valpha(1)=xi-c(1,i+nres)+c(1,i)
-                valpha(2)=yi-c(2,i+nres)+c(2,i)
-                valpha(3)=zi-c(3,i+nres)+c(3,i)
+            if (subchap.eq.1) then
+             vcat(1)=xj_temp
+             vcat(2)=yj_temp
+             vcat(3)=zj_temp
+             else
+            vcat(1)=xj_safe
+            vcat(2)=yj_safe
+            vcat(3)=zj_safe
+             endif
+            valpha(1)=xi-c(1,i+nres)+c(1,i)
+            valpha(2)=yi-c(2,i+nres)+c(2,i)
+            valpha(3)=zi-c(3,i+nres)+c(3,i)
 
 !              enddo
 
 !              enddo
-        do k=1,3
-          dx(k) = vcat(k)-vcm(k)
-        enddo
-        do k=1,3
-          v1(k)=(vcm(k)-valpha(k))
-          v2(k)=(vcat(k)-valpha(k))
-        enddo
-        v1m = sqrt(v1(1)**2+v1(2)**2+v1(3)**2)
-        v2m = sqrt(v2(1)**2+v2(2)**2+v2(3)**2)
-        v1dpv2 = v1(1)*v2(1)+v1(2)*v2(2)+v1(3)*v2(3)
+      do k=1,3
+        dx(k) = vcat(k)-vcm(k)
+      enddo
+      do k=1,3
+        v1(k)=(vcm(k)-valpha(k))
+        v2(k)=(vcat(k)-valpha(k))
+      enddo
+      v1m = sqrt(v1(1)**2+v1(2)**2+v1(3)**2)
+      v2m = sqrt(v2(1)**2+v2(2)**2+v2(3)**2)
+      v1dpv2 = v1(1)*v2(1)+v1(2)*v2(2)+v1(3)*v2(3)
 
 !  The weights of the energy function calculated from
 !The quantum mechanical GAMESS simulations of calcium with ASP/GLU
 
 !  The weights of the energy function calculated from
 !The quantum mechanical GAMESS simulations of calcium with ASP/GLU
-          if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
-            ndivi=0.5
-          else
-            ndivi=1.0
-          endif
-         ndiv=1.0
-         if ((itype(j,5).eq.1).or.(itype(j,5).eq.3)) ndiv=2.0
-
-        wh2o=78*ndivi*ndiv
-        wc = vcatprm(1)
-        wc=wc/wh2o
-        wdip =vcatprm(2)
-        wdip=wdip/wh2o
-        wquad1 =vcatprm(3)
-        wquad1=wquad1/wh2o
-        wquad2 = vcatprm(4)
-        wquad2=wquad2/wh2o
-        wquad2p = 1.0d0-wquad2
-        wvan1 = vcatprm(5)
-        wvan2 =vcatprm(6)
-        opt = dx(1)**2+dx(2)**2
-        rsecp = opt+dx(3)**2
-        rs = sqrt(rsecp)
-        rthrp = rsecp*rs
-        rfourp = rthrp*rs
-        rsixp = rfourp*rsecp
-        reight=rsixp*rsecp
-        Ir = 1.0d0/rs
-        Irsecp = 1.0d0/rsecp
-        Irthrp = Irsecp/rs
-        Irfourp = Irthrp/rs
-        Irsixp = 1.0d0/rsixp
-        Ireight=1.0d0/reight
-        Irtw=Irsixp*Irsixp
-        Irthir=Irtw/rs
-        Irfourt=Irthir/rs
-        opt1 = (4*rs*dx(3)*wdip)
-        opt2 = 6*rsecp*wquad1*opt
-        opt3 = wquad1*wquad2p*Irsixp
-        opt4 = (wvan1*wvan2**12)
-        opt5 = opt4*12*Irfourt
-        opt6 = 2*wvan1*wvan2**6
-        opt7 = 6*opt6*Ireight
-        opt8 = wdip/v1m
-        opt10 = wdip/v2m
-        opt11 = (rsecp*v2m)**2
-        opt12 = (rsecp*v1m)**2
-        opt14 = (v1m*v2m*rsecp)**2
-        opt15 = -wquad1/v2m**2
-        opt16 = (rthrp*(v1m*v2m)**2)**2
-        opt17 = (v1m**2*rthrp)**2
-        opt18 = -wquad1/rthrp
-        opt19 = (v1m**2*v2m**2)**2
-        Ec = wc*Ir
-        do k=1,3
-          dEcCat(k) = -(dx(k)*wc)*Irthrp
-          dEcCm(k)=(dx(k)*wc)*Irthrp
-          dEcCalp(k)=0.0d0
-        enddo
-        Edip=opt8*(v1dpv2)/(rsecp*v2m)
-        do k=1,3
-          dEdipCat(k)=opt8*(v1(k)*rsecp*v2m-((v2(k)/v2m &
-                     *rsecp+2*dx(k)*v2m)*v1dpv2))/opt11
-          dEdipCm(k)=opt10*(v2(k)*rsecp*v1m-((v1(k)/v1m &
-                    *rsecp-2*dx(k)*v1m)*v1dpv2))/opt12
-          dEdipCalp(k)=wdip*((-v1(k)-v2(k))*rsecp*v1m &
-                      *v2m-(-v1(k)/v1m*v2m*rsecp-v2(k)/v2m*v1m*rsecp) &
-                      *v1dpv2)/opt14
-        enddo
-        Equad1=-wquad1*v1dpv2**2/(rthrp*(v1m*v2m)**2)
-        do k=1,3
-          dEquad1Cat(k)=-wquad1*(2*v1(k)*v1dpv2*(rthrp* &
-                       (v1m*v2m)**2)-(3*dx(k)*rs*(v1m*v2m)**2+2*v1m*2* &
-                       v2(k)*1/2*1/v2m*v1m*v2m*rthrp)*v1dpv2**2)/opt16
-          dEquad1Cm(k)=-wquad1*(2*v2(k)*v1dpv2*(rthrp* &
-                      (v1m*v2m)**2)-(-3*dx(k)*rs*(v1m*v2m)**2+2*v2m*2* &
-                      v1(k)*1/2*1/v1m*v2m*v1m*rthrp)*v1dpv2**2)/opt16
-          dEquad1Calp(k)=opt18*(2*(-v1(k)-v2(k))*v1dpv2* &
-                        v1m**2*v2m**2-(-2*v1(k)*v2m**2-2*v2(k)*v1m**2)* &
-                        v1dpv2**2)/opt19
-        enddo
-        Equad2=wquad1*wquad2p*Irthrp
-        do k=1,3
-          dEquad2Cat(k)=-3*dx(k)*rs*opt3
-          dEquad2Cm(k)=3*dx(k)*rs*opt3
-          dEquad2Calp(k)=0.0d0
-        enddo
-        Evan1=opt4*Irtw
-        do k=1,3
-          dEvan1Cat(k)=-dx(k)*opt5
-          dEvan1Cm(k)=dx(k)*opt5
-          dEvan1Calp(k)=0.0d0
-        enddo
-        Evan2=-opt6*Irsixp
-        do k=1,3
-          dEvan2Cat(k)=dx(k)*opt7
-          dEvan2Cm(k)=-dx(k)*opt7
-          dEvan2Calp(k)=0.0d0
-        enddo
-        ecation_prot=ecation_prot+Ec+Edip+Equad1+Equad2+Evan1+Evan2
+        if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
+          ndivi=0.5
+        else
+          ndivi=1.0
+        endif
+       ndiv=1.0
+       if ((itype(j,5).eq.1).or.(itype(j,5).eq.3)) ndiv=2.0
+
+      wh2o=78*ndivi*ndiv
+      wc = vcatprm(1)
+      wc=wc/wh2o
+      wdip =vcatprm(2)
+      wdip=wdip/wh2o
+      wquad1 =vcatprm(3)
+      wquad1=wquad1/wh2o
+      wquad2 = vcatprm(4)
+      wquad2=wquad2/wh2o
+      wquad2p = 1.0d0-wquad2
+      wvan1 = vcatprm(5)
+      wvan2 =vcatprm(6)
+      opt = dx(1)**2+dx(2)**2
+      rsecp = opt+dx(3)**2
+      rs = sqrt(rsecp)
+      rthrp = rsecp*rs
+      rfourp = rthrp*rs
+      rsixp = rfourp*rsecp
+      reight=rsixp*rsecp
+      Ir = 1.0d0/rs
+      Irsecp = 1.0d0/rsecp
+      Irthrp = Irsecp/rs
+      Irfourp = Irthrp/rs
+      Irsixp = 1.0d0/rsixp
+      Ireight=1.0d0/reight
+      Irtw=Irsixp*Irsixp
+      Irthir=Irtw/rs
+      Irfourt=Irthir/rs
+      opt1 = (4*rs*dx(3)*wdip)
+      opt2 = 6*rsecp*wquad1*opt
+      opt3 = wquad1*wquad2p*Irsixp
+      opt4 = (wvan1*wvan2**12)
+      opt5 = opt4*12*Irfourt
+      opt6 = 2*wvan1*wvan2**6
+      opt7 = 6*opt6*Ireight
+      opt8 = wdip/v1m
+      opt10 = wdip/v2m
+      opt11 = (rsecp*v2m)**2
+      opt12 = (rsecp*v1m)**2
+      opt14 = (v1m*v2m*rsecp)**2
+      opt15 = -wquad1/v2m**2
+      opt16 = (rthrp*(v1m*v2m)**2)**2
+      opt17 = (v1m**2*rthrp)**2
+      opt18 = -wquad1/rthrp
+      opt19 = (v1m**2*v2m**2)**2
+      Ec = wc*Ir
+      do k=1,3
+        dEcCat(k) = -(dx(k)*wc)*Irthrp
+        dEcCm(k)=(dx(k)*wc)*Irthrp
+        dEcCalp(k)=0.0d0
+      enddo
+      Edip=opt8*(v1dpv2)/(rsecp*v2m)
+      do k=1,3
+        dEdipCat(k)=opt8*(v1(k)*rsecp*v2m-((v2(k)/v2m &
+                 *rsecp+2*dx(k)*v2m)*v1dpv2))/opt11
+        dEdipCm(k)=opt10*(v2(k)*rsecp*v1m-((v1(k)/v1m &
+                *rsecp-2*dx(k)*v1m)*v1dpv2))/opt12
+        dEdipCalp(k)=wdip*((-v1(k)-v2(k))*rsecp*v1m &
+                  *v2m-(-v1(k)/v1m*v2m*rsecp-v2(k)/v2m*v1m*rsecp) &
+                  *v1dpv2)/opt14
+      enddo
+      Equad1=-wquad1*v1dpv2**2/(rthrp*(v1m*v2m)**2)
+      do k=1,3
+        dEquad1Cat(k)=-wquad1*(2*v1(k)*v1dpv2*(rthrp* &
+                   (v1m*v2m)**2)-(3*dx(k)*rs*(v1m*v2m)**2+2*v1m*2* &
+                   v2(k)*1/2*1/v2m*v1m*v2m*rthrp)*v1dpv2**2)/opt16
+        dEquad1Cm(k)=-wquad1*(2*v2(k)*v1dpv2*(rthrp* &
+                  (v1m*v2m)**2)-(-3*dx(k)*rs*(v1m*v2m)**2+2*v2m*2* &
+                  v1(k)*1/2*1/v1m*v2m*v1m*rthrp)*v1dpv2**2)/opt16
+        dEquad1Calp(k)=opt18*(2*(-v1(k)-v2(k))*v1dpv2* &
+                  v1m**2*v2m**2-(-2*v1(k)*v2m**2-2*v2(k)*v1m**2)* &
+                  v1dpv2**2)/opt19
+      enddo
+      Equad2=wquad1*wquad2p*Irthrp
+      do k=1,3
+        dEquad2Cat(k)=-3*dx(k)*rs*opt3
+        dEquad2Cm(k)=3*dx(k)*rs*opt3
+        dEquad2Calp(k)=0.0d0
+      enddo
+      Evan1=opt4*Irtw
+      do k=1,3
+        dEvan1Cat(k)=-dx(k)*opt5
+        dEvan1Cm(k)=dx(k)*opt5
+        dEvan1Calp(k)=0.0d0
+      enddo
+      Evan2=-opt6*Irsixp
+      do k=1,3
+        dEvan2Cat(k)=dx(k)*opt7
+        dEvan2Cm(k)=-dx(k)*opt7
+        dEvan2Calp(k)=0.0d0
+      enddo
+      ecation_prot=ecation_prot+Ec+Edip+Equad1+Equad2+Evan1+Evan2
 !        print *,ecation_prot,Ec+Edip+Equad1+Equad2+Evan1+Evan2
 !        print *,ecation_prot,Ec+Edip+Equad1+Equad2+Evan1+Evan2
-        
-        do k=1,3
-          dEtotalCat(k)=dEcCat(k)+dEdipCat(k)+dEquad1Cat(k)+ &
-                       dEquad2Cat(k)+dEvan1Cat(k)+dEvan2Cat(k)
+      
+      do k=1,3
+        dEtotalCat(k)=dEcCat(k)+dEdipCat(k)+dEquad1Cat(k)+ &
+                   dEquad2Cat(k)+dEvan1Cat(k)+dEvan2Cat(k)
 !c             write(*,*) 'dEtotalCat inside', (dEtotalCat(l),l=1,3)
 !c             write(*,*) 'dEtotalCat inside', (dEtotalCat(l),l=1,3)
-          dEtotalCm(k)=dEcCm(k)+dEdipCm(k)+dEquad1Cm(k)+ &
-                      dEquad2Cm(k)+dEvan1Cm(k)+dEvan2Cm(k)
-          dEtotalCalp(k)=dEcCalp(k)+dEdipCalp(k)+dEquad1Calp(k) &
-                        +dEquad2Calp(k)+dEvan1Calp(k)+dEvan2Calp(k)
-        enddo
-            dscmag = 0.0d0
-            do k=1,3
-              dscvec(k) = dc(k,i+nres)
-              dscmag = dscmag+dscvec(k)*dscvec(k)
-            enddo
-            dscmag3 = dscmag
-            dscmag = sqrt(dscmag)
-            dscmag3 = dscmag3*dscmag
-            constA = 1.0d0+dASGL/dscmag
-            constB = 0.0d0
-            do k=1,3
-              constB = constB+dscvec(k)*dEtotalCm(k)
-            enddo
-            constB = constB*dASGL/dscmag3
-            do k=1,3
-              gg(k) = dEtotalCm(k)+dEtotalCalp(k)
-              gradpepcatx(k,i)=gradpepcatx(k,i)+ &
-               constA*dEtotalCm(k)-constB*dscvec(k)
+        dEtotalCm(k)=dEcCm(k)+dEdipCm(k)+dEquad1Cm(k)+ &
+                  dEquad2Cm(k)+dEvan1Cm(k)+dEvan2Cm(k)
+        dEtotalCalp(k)=dEcCalp(k)+dEdipCalp(k)+dEquad1Calp(k) &
+                  +dEquad2Calp(k)+dEvan1Calp(k)+dEvan2Calp(k)
+      enddo
+          dscmag = 0.0d0
+          do k=1,3
+            dscvec(k) = dc(k,i+nres)
+            dscmag = dscmag+dscvec(k)*dscvec(k)
+          enddo
+          dscmag3 = dscmag
+          dscmag = sqrt(dscmag)
+          dscmag3 = dscmag3*dscmag
+          constA = 1.0d0+dASGL/dscmag
+          constB = 0.0d0
+          do k=1,3
+            constB = constB+dscvec(k)*dEtotalCm(k)
+          enddo
+          constB = constB*dASGL/dscmag3
+          do k=1,3
+            gg(k) = dEtotalCm(k)+dEtotalCalp(k)
+            gradpepcatx(k,i)=gradpepcatx(k,i)+ &
+             constA*dEtotalCm(k)-constB*dscvec(k)
 !            print *,j,constA,dEtotalCm(k),constB,dscvec(k)
 !            print *,j,constA,dEtotalCm(k),constB,dscvec(k)
-              gradpepcat(k,i)=gradpepcat(k,i)+gg(k)
-              gradpepcat(k,j)=gradpepcat(k,j)+dEtotalCat(k)
-             enddo
-        else if (itype(i,1).eq.13.or.itype(i,1).eq.14) then
-           if(itype(i,1).eq.14) then
-            inum=3
-            else
-            inum=4
-            endif
-            do k=1,6
-            vcatprm(k)=catprm(k,inum)
-            enddo
-            dASGL=catprm(7,inum)
+            gradpepcat(k,i)=gradpepcat(k,i)+gg(k)
+            gradpepcat(k,j)=gradpepcat(k,j)+dEtotalCat(k)
+           enddo
+      else if (itype(i,1).eq.13.or.itype(i,1).eq.14) then
+         if(itype(i,1).eq.14) then
+          inum=3
+          else
+          inum=4
+          endif
+          do k=1,6
+          vcatprm(k)=catprm(k,inum)
+          enddo
+          dASGL=catprm(7,inum)
 !             do k=1,3
 !                vcm(k)=(cm1(k)/cm1mag)*dASGL+c(k,i+nres)
 !                valpha(k)=c(k,i)
 !                vcat(k)=c(k,j)
 !              enddo
 !             do k=1,3
 !                vcm(k)=(cm1(k)/cm1mag)*dASGL+c(k,i+nres)
 !                valpha(k)=c(k,i)
 !                vcat(k)=c(k,j)
 !              enddo
-                vcm(1)=(cm1(1)/cm1mag)*dASGL+xi
-                vcm(2)=(cm1(2)/cm1mag)*dASGL+yi
-                vcm(3)=(cm1(3)/cm1mag)*dASGL+zi
-                if (subchap.eq.1) then
-                 vcat(1)=xj_temp
-                 vcat(2)=yj_temp
-                 vcat(3)=zj_temp
-                 else
-                vcat(1)=xj_safe
-                vcat(2)=yj_safe
-                vcat(3)=zj_safe
-                endif
-                valpha(1)=xi-c(1,i+nres)+c(1,i)
-                valpha(2)=yi-c(2,i+nres)+c(2,i)
-                valpha(3)=zi-c(3,i+nres)+c(3,i)
+            vcm(1)=(cm1(1)/cm1mag)*dASGL+xi
+            vcm(2)=(cm1(2)/cm1mag)*dASGL+yi
+            vcm(3)=(cm1(3)/cm1mag)*dASGL+zi
+            if (subchap.eq.1) then
+             vcat(1)=xj_temp
+             vcat(2)=yj_temp
+             vcat(3)=zj_temp
+             else
+            vcat(1)=xj_safe
+            vcat(2)=yj_safe
+            vcat(3)=zj_safe
+            endif
+            valpha(1)=xi-c(1,i+nres)+c(1,i)
+            valpha(2)=yi-c(2,i+nres)+c(2,i)
+            valpha(3)=zi-c(3,i+nres)+c(3,i)
 
 
 
 
-        do k=1,3
-          dx(k) = vcat(k)-vcm(k)
-        enddo
-        do k=1,3
-          v1(k)=(vcm(k)-valpha(k))
-          v2(k)=(vcat(k)-valpha(k))
-        enddo
-        v1m = sqrt(v1(1)**2+v1(2)**2+v1(3)**2)
-        v2m = sqrt(v2(1)**2+v2(2)**2+v2(3)**2)
-        v1dpv2 = v1(1)*v2(1)+v1(2)*v2(2)+v1(3)*v2(3)
+      do k=1,3
+        dx(k) = vcat(k)-vcm(k)
+      enddo
+      do k=1,3
+        v1(k)=(vcm(k)-valpha(k))
+        v2(k)=(vcat(k)-valpha(k))
+      enddo
+      v1m = sqrt(v1(1)**2+v1(2)**2+v1(3)**2)
+      v2m = sqrt(v2(1)**2+v2(2)**2+v2(3)**2)
+      v1dpv2 = v1(1)*v2(1)+v1(2)*v2(2)+v1(3)*v2(3)
 !  The weights of the energy function calculated from
 !The quantum mechanical GAMESS simulations of ASN/GLN with calcium
 !  The weights of the energy function calculated from
 !The quantum mechanical GAMESS simulations of ASN/GLN with calcium
-         ndiv=1.0
-         if ((itype(j,5).eq.1).or.(itype(j,5).eq.3)) ndiv=2.0
-
-        wh2o=78*ndiv
-        wdip =vcatprm(2)
-        wdip=wdip/wh2o
-        wquad1 =vcatprm(3)
-        wquad1=wquad1/wh2o
-        wquad2 = vcatprm(4)
-        wquad2=wquad2/wh2o
-        wquad2p = 1-wquad2
-        wvan1 = vcatprm(5)
-        wvan2 =vcatprm(6)
-        opt = dx(1)**2+dx(2)**2
-        rsecp = opt+dx(3)**2
-        rs = sqrt(rsecp)
-        rthrp = rsecp*rs
-        rfourp = rthrp*rs
-        rsixp = rfourp*rsecp
-        reight=rsixp*rsecp
-        Ir = 1.0d0/rs
-        Irsecp = 1/rsecp
-        Irthrp = Irsecp/rs
-        Irfourp = Irthrp/rs
-        Irsixp = 1/rsixp
-        Ireight=1/reight
-        Irtw=Irsixp*Irsixp
-        Irthir=Irtw/rs
-        Irfourt=Irthir/rs
-        opt1 = (4*rs*dx(3)*wdip)
-        opt2 = 6*rsecp*wquad1*opt
-        opt3 = wquad1*wquad2p*Irsixp
-        opt4 = (wvan1*wvan2**12)
-        opt5 = opt4*12*Irfourt
-        opt6 = 2*wvan1*wvan2**6
-        opt7 = 6*opt6*Ireight
-        opt8 = wdip/v1m
-        opt10 = wdip/v2m
-        opt11 = (rsecp*v2m)**2
-        opt12 = (rsecp*v1m)**2
-        opt14 = (v1m*v2m*rsecp)**2
-        opt15 = -wquad1/v2m**2
-        opt16 = (rthrp*(v1m*v2m)**2)**2
-        opt17 = (v1m**2*rthrp)**2
-        opt18 = -wquad1/rthrp
-        opt19 = (v1m**2*v2m**2)**2
-        Edip=opt8*(v1dpv2)/(rsecp*v2m)
-        do k=1,3
-          dEdipCat(k)=opt8*(v1(k)*rsecp*v2m-((v2(k)/v2m&
-                     *rsecp+2*dx(k)*v2m)*v1dpv2))/opt11
-         dEdipCm(k)=opt10*(v2(k)*rsecp*v1m-((v1(k)/v1m&
-                    *rsecp-2*dx(k)*v1m)*v1dpv2))/opt12
-          dEdipCalp(k)=wdip*((-v1(k)-v2(k))*rsecp*v1m&
-                      *v2m-(-v1(k)/v1m*v2m*rsecp-v2(k)/v2m*v1m*rsecp)&
-                      *v1dpv2)/opt14
-        enddo
-        Equad1=-wquad1*v1dpv2**2/(rthrp*(v1m*v2m)**2)
-        do k=1,3
-          dEquad1Cat(k)=-wquad1*(2*v1(k)*v1dpv2*(rthrp*&
-                       (v1m*v2m)**2)-(3*dx(k)*rs*(v1m*v2m)**2+2*v1m*2*&
-                       v2(k)*1/2*1/v2m*v1m*v2m*rthrp)*v1dpv2**2)/opt16
-          dEquad1Cm(k)=-wquad1*(2*v2(k)*v1dpv2*(rthrp*&
-                      (v1m*v2m)**2)-(-3*dx(k)*rs*(v1m*v2m)**2+2*v2m*2*&
-                       v1(k)*1/2*1/v1m*v2m*v1m*rthrp)*v1dpv2**2)/opt16
-          dEquad1Calp(k)=opt18*(2*(-v1(k)-v2(k))*v1dpv2* &
-                        v1m**2*v2m**2-(-2*v1(k)*v2m**2-2*v2(k)*v1m**2)*&
-                        v1dpv2**2)/opt19
-        enddo
-        Equad2=wquad1*wquad2p*Irthrp
-        do k=1,3
-          dEquad2Cat(k)=-3*dx(k)*rs*opt3
-          dEquad2Cm(k)=3*dx(k)*rs*opt3
-          dEquad2Calp(k)=0.0d0
-        enddo
-        Evan1=opt4*Irtw
-        do k=1,3
-          dEvan1Cat(k)=-dx(k)*opt5
-          dEvan1Cm(k)=dx(k)*opt5
-          dEvan1Calp(k)=0.0d0
-        enddo
-        Evan2=-opt6*Irsixp
-        do k=1,3
-          dEvan2Cat(k)=dx(k)*opt7
-          dEvan2Cm(k)=-dx(k)*opt7
-          dEvan2Calp(k)=0.0d0
-        enddo
-         ecation_prot = ecation_prot+Edip+Equad1+Equad2+Evan1+Evan2
-        do k=1,3
-          dEtotalCat(k)=dEdipCat(k)+dEquad1Cat(k)+ &
-                       dEquad2Cat(k)+dEvan1Cat(k)+dEvan2Cat(k)
-          dEtotalCm(k)=dEdipCm(k)+dEquad1Cm(k)+ &
-                      dEquad2Cm(k)+dEvan1Cm(k)+dEvan2Cm(k)
-          dEtotalCalp(k)=dEdipCalp(k)+dEquad1Calp(k) &
-                        +dEquad2Calp(k)+dEvan1Calp(k)+dEvan2Calp(k)
-        enddo
-            dscmag = 0.0d0
-            do k=1,3
-              dscvec(k) = c(k,i+nres)-c(k,i)
+       ndiv=1.0
+       if ((itype(j,5).eq.1).or.(itype(j,5).eq.3)) ndiv=2.0
+
+      wh2o=78*ndiv
+      wdip =vcatprm(2)
+      wdip=wdip/wh2o
+      wquad1 =vcatprm(3)
+      wquad1=wquad1/wh2o
+      wquad2 = vcatprm(4)
+      wquad2=wquad2/wh2o
+      wquad2p = 1-wquad2
+      wvan1 = vcatprm(5)
+      wvan2 =vcatprm(6)
+      opt = dx(1)**2+dx(2)**2
+      rsecp = opt+dx(3)**2
+      rs = sqrt(rsecp)
+      rthrp = rsecp*rs
+      rfourp = rthrp*rs
+      rsixp = rfourp*rsecp
+      reight=rsixp*rsecp
+      Ir = 1.0d0/rs
+      Irsecp = 1/rsecp
+      Irthrp = Irsecp/rs
+      Irfourp = Irthrp/rs
+      Irsixp = 1/rsixp
+      Ireight=1/reight
+      Irtw=Irsixp*Irsixp
+      Irthir=Irtw/rs
+      Irfourt=Irthir/rs
+      opt1 = (4*rs*dx(3)*wdip)
+      opt2 = 6*rsecp*wquad1*opt
+      opt3 = wquad1*wquad2p*Irsixp
+      opt4 = (wvan1*wvan2**12)
+      opt5 = opt4*12*Irfourt
+      opt6 = 2*wvan1*wvan2**6
+      opt7 = 6*opt6*Ireight
+      opt8 = wdip/v1m
+      opt10 = wdip/v2m
+      opt11 = (rsecp*v2m)**2
+      opt12 = (rsecp*v1m)**2
+      opt14 = (v1m*v2m*rsecp)**2
+      opt15 = -wquad1/v2m**2
+      opt16 = (rthrp*(v1m*v2m)**2)**2
+      opt17 = (v1m**2*rthrp)**2
+      opt18 = -wquad1/rthrp
+      opt19 = (v1m**2*v2m**2)**2
+      Edip=opt8*(v1dpv2)/(rsecp*v2m)
+      do k=1,3
+        dEdipCat(k)=opt8*(v1(k)*rsecp*v2m-((v2(k)/v2m&
+                 *rsecp+2*dx(k)*v2m)*v1dpv2))/opt11
+       dEdipCm(k)=opt10*(v2(k)*rsecp*v1m-((v1(k)/v1m&
+                *rsecp-2*dx(k)*v1m)*v1dpv2))/opt12
+        dEdipCalp(k)=wdip*((-v1(k)-v2(k))*rsecp*v1m&
+                  *v2m-(-v1(k)/v1m*v2m*rsecp-v2(k)/v2m*v1m*rsecp)&
+                  *v1dpv2)/opt14
+      enddo
+      Equad1=-wquad1*v1dpv2**2/(rthrp*(v1m*v2m)**2)
+      do k=1,3
+        dEquad1Cat(k)=-wquad1*(2*v1(k)*v1dpv2*(rthrp*&
+                   (v1m*v2m)**2)-(3*dx(k)*rs*(v1m*v2m)**2+2*v1m*2*&
+                   v2(k)*1/2*1/v2m*v1m*v2m*rthrp)*v1dpv2**2)/opt16
+        dEquad1Cm(k)=-wquad1*(2*v2(k)*v1dpv2*(rthrp*&
+                  (v1m*v2m)**2)-(-3*dx(k)*rs*(v1m*v2m)**2+2*v2m*2*&
+                   v1(k)*1/2*1/v1m*v2m*v1m*rthrp)*v1dpv2**2)/opt16
+        dEquad1Calp(k)=opt18*(2*(-v1(k)-v2(k))*v1dpv2* &
+                  v1m**2*v2m**2-(-2*v1(k)*v2m**2-2*v2(k)*v1m**2)*&
+                  v1dpv2**2)/opt19
+      enddo
+      Equad2=wquad1*wquad2p*Irthrp
+      do k=1,3
+        dEquad2Cat(k)=-3*dx(k)*rs*opt3
+        dEquad2Cm(k)=3*dx(k)*rs*opt3
+        dEquad2Calp(k)=0.0d0
+      enddo
+      Evan1=opt4*Irtw
+      do k=1,3
+        dEvan1Cat(k)=-dx(k)*opt5
+        dEvan1Cm(k)=dx(k)*opt5
+        dEvan1Calp(k)=0.0d0
+      enddo
+      Evan2=-opt6*Irsixp
+      do k=1,3
+        dEvan2Cat(k)=dx(k)*opt7
+        dEvan2Cm(k)=-dx(k)*opt7
+        dEvan2Calp(k)=0.0d0
+      enddo
+       ecation_prot = ecation_prot+Edip+Equad1+Equad2+Evan1+Evan2
+      do k=1,3
+        dEtotalCat(k)=dEdipCat(k)+dEquad1Cat(k)+ &
+                   dEquad2Cat(k)+dEvan1Cat(k)+dEvan2Cat(k)
+        dEtotalCm(k)=dEdipCm(k)+dEquad1Cm(k)+ &
+                  dEquad2Cm(k)+dEvan1Cm(k)+dEvan2Cm(k)
+        dEtotalCalp(k)=dEdipCalp(k)+dEquad1Calp(k) &
+                  +dEquad2Calp(k)+dEvan1Calp(k)+dEvan2Calp(k)
+      enddo
+          dscmag = 0.0d0
+          do k=1,3
+            dscvec(k) = c(k,i+nres)-c(k,i)
 ! TU SPRAWDZ???
 !              dscvec(1) = xj
 !              dscvec(2) = yj
 !              dscvec(3) = zj
 
 ! TU SPRAWDZ???
 !              dscvec(1) = xj
 !              dscvec(2) = yj
 !              dscvec(3) = zj
 
-              dscmag = dscmag+dscvec(k)*dscvec(k)
-            enddo
-            dscmag3 = dscmag
-            dscmag = sqrt(dscmag)
-            dscmag3 = dscmag3*dscmag
-            constA = 1+dASGL/dscmag
-            constB = 0.0d0
-            do k=1,3
-              constB = constB+dscvec(k)*dEtotalCm(k)
-            enddo
-            constB = constB*dASGL/dscmag3
-            do k=1,3
-              gg(k) = dEtotalCm(k)+dEtotalCalp(k)
-              gradpepcatx(k,i)=gradpepcatx(k,i)+ &
-               constA*dEtotalCm(k)-constB*dscvec(k)
-              gradpepcat(k,i)=gradpepcat(k,i)+gg(k)
-              gradpepcat(k,j)=gradpepcat(k,j)+dEtotalCat(k)
-             enddo
-           else
-            rcal = 0.0d0
-            do k=1,3
+            dscmag = dscmag+dscvec(k)*dscvec(k)
+          enddo
+          dscmag3 = dscmag
+          dscmag = sqrt(dscmag)
+          dscmag3 = dscmag3*dscmag
+          constA = 1+dASGL/dscmag
+          constB = 0.0d0
+          do k=1,3
+            constB = constB+dscvec(k)*dEtotalCm(k)
+          enddo
+          constB = constB*dASGL/dscmag3
+          do k=1,3
+            gg(k) = dEtotalCm(k)+dEtotalCalp(k)
+            gradpepcatx(k,i)=gradpepcatx(k,i)+ &
+             constA*dEtotalCm(k)-constB*dscvec(k)
+            gradpepcat(k,i)=gradpepcat(k,i)+gg(k)
+            gradpepcat(k,j)=gradpepcat(k,j)+dEtotalCat(k)
+           enddo
+         else
+          rcal = 0.0d0
+          do k=1,3
 !              r(k) = c(k,j)-c(k,i+nres)
 !              r(k) = c(k,j)-c(k,i+nres)
-              r(1) = xj
-              r(2) = yj
-              r(3) = zj
-              rcal = rcal+r(k)*r(k)
-            enddo
-            ract=sqrt(rcal)
-            rocal=1.5
-            epscalc=0.2
-            r0p=0.5*(rocal+sig0(itype(i,1)))
-            r06 = r0p**6
-            r012 = r06*r06
-            Evan1=epscalc*(r012/rcal**6)
-            Evan2=epscalc*2*(r06/rcal**3)
-            r4 = rcal**4
-            r7 = rcal**7
-            do k=1,3
-              dEvan1Cm(k) = 12*r(k)*epscalc*r012/r7
-              dEvan2Cm(k) = 12*r(k)*epscalc*r06/r4
-            enddo
-            do k=1,3
-              dEtotalCm(k)=dEvan1Cm(k)+dEvan2Cm(k)
-            enddo
-                 ecation_prot = ecation_prot+ Evan1+Evan2
-            do  k=1,3
-               gradpepcatx(k,i)=gradpepcatx(k,i)+ & 
-               dEtotalCm(k)
-              gradpepcat(k,i)=gradpepcat(k,i)+dEtotalCm(k)
-              gradpepcat(k,j)=gradpepcat(k,j)-dEtotalCm(k)
-             enddo
-         endif ! 13-16 residues
+            r(1) = xj
+            r(2) = yj
+            r(3) = zj
+            rcal = rcal+r(k)*r(k)
+          enddo
+          ract=sqrt(rcal)
+          rocal=1.5
+          epscalc=0.2
+          r0p=0.5*(rocal+sig0(itype(i,1)))
+          r06 = r0p**6
+          r012 = r06*r06
+          Evan1=epscalc*(r012/rcal**6)
+          Evan2=epscalc*2*(r06/rcal**3)
+          r4 = rcal**4
+          r7 = rcal**7
+          do k=1,3
+            dEvan1Cm(k) = 12*r(k)*epscalc*r012/r7
+            dEvan2Cm(k) = 12*r(k)*epscalc*r06/r4
+          enddo
+          do k=1,3
+            dEtotalCm(k)=dEvan1Cm(k)+dEvan2Cm(k)
+          enddo
+             ecation_prot = ecation_prot+ Evan1+Evan2
+          do  k=1,3
+             gradpepcatx(k,i)=gradpepcatx(k,i)+ & 
+             dEtotalCm(k)
+            gradpepcat(k,i)=gradpepcat(k,i)+dEtotalCm(k)
+            gradpepcat(k,j)=gradpepcat(k,j)-dEtotalCm(k)
+           enddo
+       endif ! 13-16 residues
        enddo !j
        enddo !i
        return
        end subroutine ecat_prot
 
 !----------------------------------------------------------------------------
        enddo !j
        enddo !i
        return
        end subroutine ecat_prot
 
 !----------------------------------------------------------------------------
+!---------------------------------------------------------------------------
+       subroutine ecat_nucl(ecation_nucl)
+       integer i,j,k,subchap,itmp,inum,itypi,itypj
+       real(kind=8) :: xi,yi,zi,xj,yj,zj
+       real(kind=8) xj_temp,yj_temp,zj_temp,xj_safe,yj_safe,zj_safe, &
+       dist_init,dist_temp,ecation_nucl,Evan1,Evan2,Ecav,Egb,wdip1,wdip2, &
+       wvan1,wvan2,wgbsig,wgbeps,wgbchi,wgbchip,wcav1,wcav2,wcav3,wcav4, &
+       wcavsig,wcavchi,v1m,v1dpdx,wh2o,wc,Edip,rcs2,invrcs6,invrcs8,invrcs12, &
+       invrcs14,rcb,rcb2,invrcb,invrcb2,invrcb4,invrcb6,cosinus,cos2,dcosdcatconst, &
+       dcosdcalpconst,dcosdcmconst,rcav,rcav11,rcav12,constcav1,constcav2, &
+       constgb1,constgb2,constdvan1,constdvan2,sgb,sgb6,sgb7,sgb12,sgb13, &
+       cavnum,cavdenom,invcavdenom2,dcavnumdcos,dcavnumdr,dcavdenomdcos, &
+       dcavdenomdr,sslipi,ssgradlipi,sslipj,ssgradlipj,aa,bb
+       real(kind=8),dimension(3) ::gg,r,dEtotalCm,dEtotalCalp,dEvan1Cm,&
+       dEvan2Cm,cm1,cm,vcat,vsug,v1,v2,dx,vcm,dEdipCm,dEdipCalp, &
+       dEvan1Calp,dEvan2Cat,dEvan2Calp,dEtotalCat,dEdipCat,dEvan1Cat,dcosdcat, &
+       dcosdcalp,dcosdcm,dEgbdCat,dEgbdCalp,dEgbdCm,dEcavdCat,dEcavdCalp, &
+       dEcavdCm,boxik
+       real(kind=8),dimension(14) :: vcatnuclprm
+       ecation_nucl=0.0d0
+       boxik(1)=boxxsize
+       boxik(2)=boxysize
+       boxik(3)=boxzsize
+
+       if (nres_molec(5).eq.0) return
+       itmp=0
+       do i=1,4
+          itmp=itmp+nres_molec(i)
+       enddo
+       do i=iatsc_s_nucl,iatsc_e_nucl
+          if ((itype(i,2).eq.ntyp1_molec(2))) cycle ! leave dummy atoms
+          xi=(c(1,i+nres))
+          yi=(c(2,i+nres))
+          zi=(c(3,i+nres))
+      call to_box(xi,yi,zi)
+      call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+          do k=1,3
+             cm1(k)=dc(k,i+nres)
+          enddo
+          do j=itmp+1,itmp+nres_molec(5)
+             xj=c(1,j)
+             yj=c(2,j)
+             zj=c(3,j)
+      call to_box(xj,yj,zj)
+!      write(iout,*) "xi,yi,zi,xj,yj,zj", xi,yi,zi,xj,yj,zj
+!      call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+!      aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+!       +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+!      bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+!       +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)
+!       write(iout,*) 'after shift', xj,yj,zj
+             dist_init=xj**2+yj**2+zj**2
+
+             itypi=itype(i,2)
+             itypj=itype(j,5)
+             do k=1,13
+                vcatnuclprm(k)=catnuclprm(k,itypi,itypj)
+             enddo
+             do k=1,3
+                vcm(k)=c(k,i+nres)
+                vsug(k)=c(k,i)
+                vcat(k)=c(k,j)
+             enddo
+             call to_box(vcm(1),vcm(2),vcm(3))
+             call to_box(vsug(1),vsug(2),vsug(3))
+             call to_box(vcat(1),vcat(2),vcat(3))
+             do k=1,3
+!                dx(k) = vcat(k)-vcm(k)
+!             enddo
+                dx(k)=boxshift(vcat(k)-vcm(k),boxik(k))            
+!             do k=1,3
+                v1(k)=dc(k,i+nres)
+                v2(k)=boxshift(vcat(k)-vsug(k),boxik(k))
+             enddo
+             v1m = sqrt(v1(1)**2+v1(2)**2+v1(3)**2)
+             v1dpdx = v1(1)*dx(1)+v1(2)*dx(2)+v1(3)*dx(3)
+!  The weights of the energy function calculated from
+!The quantum mechanical Gaussian simulations of potassium and sodium with deoxynucleosides
+             wh2o=78
+             wdip1 = vcatnuclprm(1)
+             wdip1 = wdip1/wh2o                     !w1
+             wdip2 = vcatnuclprm(2)
+             wdip2 = wdip2/wh2o                     !w2
+             wvan1 = vcatnuclprm(3)
+             wvan2 = vcatnuclprm(4)                 !pis1
+             wgbsig = vcatnuclprm(5)                !sigma0
+             wgbeps = vcatnuclprm(6)                !epsi0
+             wgbchi = vcatnuclprm(7)                !chi1
+             wgbchip = vcatnuclprm(8)               !chip1
+             wcavsig = vcatnuclprm(9)               !sig
+             wcav1 = vcatnuclprm(10)                !b1
+             wcav2 = vcatnuclprm(11)                !b2
+             wcav3 = vcatnuclprm(12)                !b3
+             wcav4 = vcatnuclprm(13)                !b4
+             wcavchi = vcatnuclprm(14)              !chis1
+             rcs2 = v2(1)**2+v2(2)**2+v2(3)**2
+             invrcs6 = 1/rcs2**3
+             invrcs8 = invrcs6/rcs2
+             invrcs12 = invrcs6**2
+             invrcs14 = invrcs12/rcs2
+             rcb2 = dx(1)**2+dx(2)**2+dx(3)**2
+             rcb = sqrt(rcb2)
+             invrcb = 1/rcb
+             invrcb2 = invrcb**2
+             invrcb4 = invrcb2**2
+             invrcb6 = invrcb4*invrcb2
+             cosinus = v1dpdx/(v1m*rcb)
+             cos2 = cosinus**2
+             dcosdcatconst = invrcb2/v1m
+             dcosdcalpconst = invrcb/v1m**2
+             dcosdcmconst = invrcb2/v1m**2
+             do k=1,3
+                dcosdcat(k) = (v1(k)*rcb-dx(k)*v1m*cosinus)*dcosdcatconst
+                dcosdcalp(k) = (v1(k)*rcb*cosinus-dx(k)*v1m)*dcosdcalpconst
+                dcosdcm(k) = ((dx(k)-v1(k))*v1m*rcb+ &
+                        cosinus*(dx(k)*v1m**2-v1(k)*rcb2))*dcosdcmconst
+             enddo
+             rcav = rcb/wcavsig
+             rcav11 = rcav**11
+             rcav12 = rcav11*rcav
+             constcav1 = 1-wcavchi*cos2
+             constcav2 = sqrt(constcav1)
+             constgb1 = 1/sqrt(1-wgbchi*cos2)
+             constgb2 = wgbeps*(1-wgbchip*cos2)**2
+             constdvan1 = 12*wvan1*wvan2**12*invrcs14
+             constdvan2 = 6*wvan1*wvan2**6*invrcs8
+!----------------------------------------------------------------------------
+!Gay-Berne term
+!---------------------------------------------------------------------------
+             sgb = 1/(1-constgb1+(rcb/wgbsig))
+             sgb6 = sgb**6
+             sgb7 = sgb6*sgb
+             sgb12 = sgb6**2
+             sgb13 = sgb12*sgb
+             Egb = constgb2*(sgb12-sgb6)
+             do k=1,3
+                dEgbdCat(k) = -constgb2/wgbsig*(12*sgb13-6*sgb7)*invrcb*dx(k) &
+                 +(constgb1**3*constgb2*wgbchi*cosinus*(12*sgb13-6*sgb7) &
+     -4*wgbeps*wgbchip*cosinus*(1-wgbchip*cos2)*(sgb12-sgb6))*dcosdcat(k)
+                dEgbdCm(k) = constgb2/wgbsig*(12*sgb13-6*sgb7)*invrcb*dx(k) &
+                 +(constgb1**3*constgb2*wgbchi*cosinus*(12*sgb13-6*sgb7) &
+     -4*wgbeps*wgbchip*cosinus*(1-wgbchip*cos2)*(sgb12-sgb6))*dcosdcm(k)
+                dEgbdCalp(k) = (constgb1**3*constgb2*wgbchi*cosinus &
+                               *(12*sgb13-6*sgb7) &
+     -4*wgbeps*wgbchip*cosinus*(1-wgbchip*cos2)*(sgb12-sgb6))*dcosdcalp(k)
+             enddo
+!----------------------------------------------------------------------------
+!cavity term
+!---------------------------------------------------------------------------
+             cavnum = sqrt(rcav*constcav2)+wcav2*rcav*constcav2-wcav3
+             cavdenom = 1+wcav4*rcav12*constcav1**6
+             Ecav = wcav1*cavnum/cavdenom
+             invcavdenom2 = 1/cavdenom**2
+             dcavnumdcos = -wcavchi*cosinus/constcav2 &
+                    *(sqrt(rcav/constcav2)/2+wcav2*rcav)
+             dcavnumdr = (0.5*sqrt(constcav2/rcav)+wcav2*constcav2)/wcavsig
+             dcavdenomdcos = -12*wcav4*wcavchi*rcav12*constcav1**5*cosinus
+             dcavdenomdr = 12*wcav4/wcavsig*rcav11*constcav1**6
+             do k=1,3
+                dEcavdCat(k) = ((dcavnumdcos*cavdenom-dcavdenomdcos*cavnum) &
+     *dcosdcat(k)+(dcavnumdr*cavdenom-dcavdenomdr*cavnum)/rcb*dx(k))*wcav1*invcavdenom2
+                dEcavdCm(k) = ((dcavnumdcos*cavdenom-dcavdenomdcos*cavnum) &
+     *dcosdcm(k)-(dcavnumdr*cavdenom-dcavdenomdr*cavnum)/rcb*dx(k))*wcav1*invcavdenom2
+                dEcavdCalp(k) = (dcavnumdcos*cavdenom-dcavdenomdcos*cavnum) &
+                             *dcosdcalp(k)*wcav1*invcavdenom2
+             enddo
+!----------------------------------------------------------------------------
+!van der Waals and dipole-charge interaction energy
+!---------------------------------------------------------------------------
+             Evan1 = wvan1*wvan2**12*invrcs12
+             do k=1,3
+                dEvan1Cat(k) = -v2(k)*constdvan1
+                dEvan1Cm(k) = 0.0d0
+                dEvan1Calp(k) = v2(k)*constdvan1
+             enddo
+             Evan2 = -wvan1*wvan2**6*invrcs6
+             do k=1,3
+                dEvan2Cat(k) = v2(k)*constdvan2
+                dEvan2Cm(k) = 0.0d0
+                dEvan2Calp(k) = -v2(k)*constdvan2
+             enddo
+             Edip = wdip1*cosinus*invrcb2-wdip2*(1-cos2)*invrcb4
+             do k=1,3
+                dEdipCat(k) = (-2*wdip1*cosinus*invrcb4 &
+                               +4*wdip2*(1-cos2)*invrcb6)*dx(k) &
+                   +dcosdcat(k)*(wdip1*invrcb2+2*wdip2*cosinus*invrcb4)
+                dEdipCm(k) = (2*wdip1*cosinus*invrcb4 &
+                             -4*wdip2*(1-cos2)*invrcb6)*dx(k) &
+                   +dcosdcm(k)*(wdip1*invrcb2+2*wdip2*cosinus*invrcb4)
+                dEdipCalp(k) = dcosdcalp(k)*(wdip1*invrcb2 &
+                                  +2*wdip2*cosinus*invrcb4)
+             enddo
+             if (energy_dec) write (iout,'(2i5,4(a6,f7.3))') i,j, &
+         ' E GB ',Egb,' ECav ',Ecav,' Evdw ',Evan1+Evan2,' Edip ',Edip
+             ecation_nucl=ecation_nucl+Ecav+Egb+Edip+Evan1+Evan2
+             do k=1,3
+                dEtotalCat(k) = dEcavdCat(k)+dEvan1Cat(k)+dEvan2Cat(k) &
+                                             +dEgbdCat(k)+dEdipCat(k)
+                dEtotalCm(k) = dEcavdCm(k)+dEvan1Cm(k)+dEvan2Cm(k) &
+                                           +dEgbdCm(k)+dEdipCm(k)
+                dEtotalCalp(k) = dEcavdCalp(k)+dEgbdCalp(k)+dEvan1Calp(k) &
+                                             +dEdipCalp(k)+dEvan2Calp(k)
+             enddo
+             do k=1,3
+                gg(k) = dEtotalCm(k)+dEtotalCalp(k)
+                gradnuclcatx(k,i)=gradnuclcatx(k,i)+dEtotalCm(k)
+                gradnuclcat(k,i)=gradnuclcat(k,i)+gg(k)
+                gradnuclcat(k,j)=gradnuclcat(k,j)+dEtotalCat(k)
+             enddo
+          enddo !j
+       enddo !i
+       return
+       end subroutine ecat_nucl
+
 !-----------------------------------------------------------------------------
 !-----------------------------------------------------------------------------
       subroutine eprot_sc_base(escbase)
 !-----------------------------------------------------------------------------
 !-----------------------------------------------------------------------------
       subroutine eprot_sc_base(escbase)
@@ -23760,128 +23802,96 @@
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
       real(kind=8) :: evdw,sig0ij
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
       real(kind=8) :: evdw,sig0ij
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
-                    dist_temp, dist_init,aa,bb,ssgradlipi,ssgradlipj, &
-                    sslipi,sslipj,faclip
+                dist_temp, dist_init,aa,bb,ssgradlipi,ssgradlipj, &
+                sslipi,sslipj,faclip
       integer :: ii
       real(kind=8) :: fracinbuf
        real (kind=8) :: escbase
        real (kind=8),dimension(4):: ener
        real(kind=8) :: b1,b2,b3,b4,egb,eps_in,eps_inout_fac,eps_out
        real(kind=8) :: ECL,Elj,Equad,Epol,eheadtail,rhead,dGCLOM2,&
       integer :: ii
       real(kind=8) :: fracinbuf
        real (kind=8) :: escbase
        real (kind=8),dimension(4):: ener
        real(kind=8) :: b1,b2,b3,b4,egb,eps_in,eps_inout_fac,eps_out
        real(kind=8) :: ECL,Elj,Equad,Epol,eheadtail,rhead,dGCLOM2,&
-        sqom1,sqom2,sqom12,c1,c2,c3,pom,Lambf,sparrow,&
-        Chif,ChiLambf,bat,eagle,top,bot,botsq,Fcav,dtop,dFdR,dFdOM1,&
-        dFdOM2,w1,w2,w3,dGCLdR,dFdL,dFdOM12,dbot ,&
-        r1,eps_head,alphapol1,pis,facd2,d2,facd1,d1,erdxj,erdxi,federmaus,&
-        dPOLdR1,dFGBdOM2,dFGBdR1,dPOLdFGB1,RR1,MomoFac1,hawk,d1i,d1j,&
-        sig1,sig2,chis12,chis2,ee1,fgb1,a12sq,chis1
+      sqom1,sqom2,sqom12,c1,c2,c3,pom,Lambf,sparrow,&
+      Chif,ChiLambf,bat,eagle,top,bot,botsq,Fcav,dtop,dFdR,dFdOM1,&
+      dFdOM2,w1,w2,w3,dGCLdR,dFdL,dFdOM12,dbot ,&
+      r1,eps_head,alphapol1,pis,facd2,d2,facd1,d1,erdxj,erdxi,federmaus,&
+      dPOLdR1,dFGBdOM2,dFGBdR1,dPOLdFGB1,RR1,MomoFac1,hawk,d1i,d1j,&
+      sig1,sig2,chis12,chis2,ee1,fgb1,a12sq,chis1
        real(kind=8),dimension(3,2)::chead,erhead_tail
        real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead
        integer troll
        eps_out=80.0d0
        escbase=0.0d0
 !       do i=1,nres_molec(1)
        real(kind=8),dimension(3,2)::chead,erhead_tail
        real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead
        integer troll
        eps_out=80.0d0
        escbase=0.0d0
 !       do i=1,nres_molec(1)
-        do i=ibond_start,ibond_end
-        if (itype(i,1).eq.ntyp1_molec(1)) cycle
-        itypi  = itype(i,1)
-        dxi    = dc_norm(1,nres+i)
-        dyi    = dc_norm(2,nres+i)
-        dzi    = dc_norm(3,nres+i)
-        dsci_inv = vbld_inv(i+nres)
-        xi=c(1,nres+i)
-        yi=c(2,nres+i)
-        zi=c(3,nres+i)
-        xi=mod(xi,boxxsize)
-         if (xi.lt.0) xi=xi+boxxsize
-        yi=mod(yi,boxysize)
-         if (yi.lt.0) yi=yi+boxysize
-        zi=mod(zi,boxzsize)
-         if (zi.lt.0) zi=zi+boxzsize
-         do j=nres_molec(1)+1,nres_molec(2)+nres_molec(1)
-           itypj= itype(j,2)
-           if (itype(j,2).eq.ntyp1_molec(2))cycle
-           xj=c(1,j+nres)
-           yj=c(2,j+nres)
-           zj=c(3,j+nres)
-           xj=dmod(xj,boxxsize)
-           if (xj.lt.0) xj=xj+boxxsize
-           yj=dmod(yj,boxysize)
-           if (yj.lt.0) yj=yj+boxysize
-           zj=dmod(zj,boxzsize)
-           if (zj.lt.0) zj=zj+boxzsize
-          dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          xj_safe=xj
-          yj_safe=yj
-          zj_safe=zj
-          subchap=0
-
-          do xshift=-1,1
-          do yshift=-1,1
-          do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-          enddo
-          enddo
-          enddo
-          if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-          else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-          endif
-          dxj = dc_norm( 1, nres+j )
-          dyj = dc_norm( 2, nres+j )
-          dzj = dc_norm( 3, nres+j )
+      do i=ibond_start,ibond_end
+      if (itype(i,1).eq.ntyp1_molec(1)) cycle
+      itypi  = itype(i,1)
+      dxi    = dc_norm(1,nres+i)
+      dyi    = dc_norm(2,nres+i)
+      dzi    = dc_norm(3,nres+i)
+      dsci_inv = vbld_inv(i+nres)
+      xi=c(1,nres+i)
+      yi=c(2,nres+i)
+      zi=c(3,nres+i)
+      call to_box(xi,yi,zi)
+      call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+       do j=nres_molec(1)+1,nres_molec(2)+nres_molec(1)
+         itypj= itype(j,2)
+         if (itype(j,2).eq.ntyp1_molec(2))cycle
+         xj=c(1,j+nres)
+         yj=c(2,j+nres)
+         zj=c(3,j+nres)
+      call to_box(xj,yj,zj)
+!      call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+!      aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+!       +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+!      bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+!       +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)
+
+        dxj = dc_norm( 1, nres+j )
+        dyj = dc_norm( 2, nres+j )
+        dzj = dc_norm( 3, nres+j )
 !          print *,i,j,itypi,itypj
 !          print *,i,j,itypi,itypj
-          d1i = dhead_scbasei(itypi,itypj) !this is shift of dipole/charge
-          d1j = dhead_scbasej(itypi,itypj) !this is shift of dipole/charge
+        d1i = dhead_scbasei(itypi,itypj) !this is shift of dipole/charge
+        d1j = dhead_scbasej(itypi,itypj) !this is shift of dipole/charge
 !          d1i=0.0d0
 !          d1j=0.0d0
 !          BetaT = 1.0d0 / (298.0d0 * Rb)
 ! Gay-berne var's
 !          d1i=0.0d0
 !          d1j=0.0d0
 !          BetaT = 1.0d0 / (298.0d0 * Rb)
 ! Gay-berne var's
-          sig0ij = sigma_scbase( itypi,itypj )
-          chi1   = chi_scbase( itypi, itypj,1 )
-          chi2   = chi_scbase( itypi, itypj,2 )
+        sig0ij = sigma_scbase( itypi,itypj )
+        chi1   = chi_scbase( itypi, itypj,1 )
+        chi2   = chi_scbase( itypi, itypj,2 )
 !          chi1=0.0d0
 !          chi2=0.0d0
 !          chi1=0.0d0
 !          chi2=0.0d0
-          chi12  = chi1 * chi2
-          chip1  = chipp_scbase( itypi, itypj,1 )
-          chip2  = chipp_scbase( itypi, itypj,2 )
+        chi12  = chi1 * chi2
+        chip1  = chipp_scbase( itypi, itypj,1 )
+        chip2  = chipp_scbase( itypi, itypj,2 )
 !          chip1=0.0d0
 !          chip2=0.0d0
 !          chip1=0.0d0
 !          chip2=0.0d0
-          chip12 = chip1 * chip2
+        chip12 = chip1 * chip2
 ! not used by momo potential, but needed by sc_angular which is shared
 ! by all energy_potential subroutines
 ! not used by momo potential, but needed by sc_angular which is shared
 ! by all energy_potential subroutines
-          alf1   = 0.0d0
-          alf2   = 0.0d0
-          alf12  = 0.0d0
-          a12sq = rborn_scbasei(itypi,itypj) * rborn_scbasej(itypi,itypj)
+        alf1   = 0.0d0
+        alf2   = 0.0d0
+        alf12  = 0.0d0
+        a12sq = rborn_scbasei(itypi,itypj) * rborn_scbasej(itypi,itypj)
 !       a12sq = a12sq * a12sq
 ! charge of amino acid itypi is...
 !       a12sq = a12sq * a12sq
 ! charge of amino acid itypi is...
-          chis1 = chis_scbase(itypi,itypj,1)
-          chis2 = chis_scbase(itypi,itypj,2)
-          chis12 = chis1 * chis2
-          sig1 = sigmap1_scbase(itypi,itypj)
-          sig2 = sigmap2_scbase(itypi,itypj)
+        chis1 = chis_scbase(itypi,itypj,1)
+        chis2 = chis_scbase(itypi,itypj,2)
+        chis12 = chis1 * chis2
+        sig1 = sigmap1_scbase(itypi,itypj)
+        sig2 = sigmap2_scbase(itypi,itypj)
 !       write (*,*) "sig1 = ", sig1
 !       write (*,*) "sig2 = ", sig2
 ! alpha factors from Fcav/Gcav
 !       write (*,*) "sig1 = ", sig1
 !       write (*,*) "sig2 = ", sig2
 ! alpha factors from Fcav/Gcav
-          b1 = alphasur_scbase(1,itypi,itypj)
+        b1 = alphasur_scbase(1,itypi,itypj)
 !          b1=0.0d0
 !          b1=0.0d0
-          b2 = alphasur_scbase(2,itypi,itypj)
-          b3 = alphasur_scbase(3,itypi,itypj)
-          b4 = alphasur_scbase(4,itypi,itypj)
+        b2 = alphasur_scbase(2,itypi,itypj)
+        b3 = alphasur_scbase(3,itypi,itypj)
+        b4 = alphasur_scbase(4,itypi,itypj)
 ! used to determine whether we want to do quadrupole calculations
 ! used by Fgb
        eps_in = epsintab_scbase(itypi,itypj)
 ! used to determine whether we want to do quadrupole calculations
 ! used by Fgb
        eps_in = epsintab_scbase(itypi,itypj)
@@ -23894,18 +23904,18 @@
 ! location of polar head is computed by taking hydrophobic centre
 ! and moving by a d1 * dc_norm vector
 ! see unres publications for very informative images
 ! location of polar head is computed by taking hydrophobic centre
 ! and moving by a d1 * dc_norm vector
 ! see unres publications for very informative images
-        chead(k,1) = c(k, i+nres) + d1i * dc_norm(k, i+nres)
-        chead(k,2) = c(k, j+nres) + d1j * dc_norm(k, j+nres)
+      chead(k,1) = c(k, i+nres) + d1i * dc_norm(k, i+nres)
+      chead(k,2) = c(k, j+nres) + d1j * dc_norm(k, j+nres)
 ! distance 
 !        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
 !        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
 ! distance 
 !        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
 !        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
-        Rhead_distance(k) = chead(k,2) - chead(k,1)
+      Rhead_distance(k) = chead(k,2) - chead(k,1)
        END DO
 ! pitagoras (root of sum of squares)
        Rhead = dsqrt( &
        END DO
 ! pitagoras (root of sum of squares)
        Rhead = dsqrt( &
-          (Rhead_distance(1)*Rhead_distance(1)) &
-        + (Rhead_distance(2)*Rhead_distance(2)) &
-        + (Rhead_distance(3)*Rhead_distance(3)))
+        (Rhead_distance(1)*Rhead_distance(1)) &
+      + (Rhead_distance(2)*Rhead_distance(2)) &
+      + (Rhead_distance(3)*Rhead_distance(3)))
 !-------------------------------------------------------------------
 ! zero everything that should be zero'ed
        evdwij = 0.0d0
 !-------------------------------------------------------------------
 ! zero everything that should be zero'ed
        evdwij = 0.0d0
@@ -23920,95 +23930,95 @@
        dGCLdOM12 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0
        dGCLdOM12 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0
-          Fcav = 0.0d0
-          dFdR = 0.0d0
-          dCAVdOM1  = 0.0d0
-          dCAVdOM2  = 0.0d0
-          dCAVdOM12 = 0.0d0
-          dscj_inv = vbld_inv(j+nres)
+        Fcav = 0.0d0
+        dFdR = 0.0d0
+        dCAVdOM1  = 0.0d0
+        dCAVdOM2  = 0.0d0
+        dCAVdOM12 = 0.0d0
+        dscj_inv = vbld_inv(j+nres)
 !          print *,i,j,dscj_inv,dsci_inv
 ! rij holds 1/(distance of Calpha atoms)
 !          print *,i,j,dscj_inv,dsci_inv
 ! rij holds 1/(distance of Calpha atoms)
-          rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
-          rij  = dsqrt(rrij)
+        rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
+        rij  = dsqrt(rrij)
 !----------------------------
 !----------------------------
-          CALL sc_angular
+        CALL sc_angular
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials
 ! om = omega, sqom = om^2
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials
 ! om = omega, sqom = om^2
-          sqom1  = om1 * om1
-          sqom2  = om2 * om2
-          sqom12 = om12 * om12
+        sqom1  = om1 * om1
+        sqom2  = om2 * om2
+        sqom12 = om12 * om12
 
 ! now we calculate EGB - Gey-Berne
 ! It will be summed up in evdwij and saved in evdw
 
 ! now we calculate EGB - Gey-Berne
 ! It will be summed up in evdwij and saved in evdw
-          sigsq     = 1.0D0  / sigsq
-          sig       = sig0ij * dsqrt(sigsq)
+        sigsq     = 1.0D0  / sigsq
+        sig       = sig0ij * dsqrt(sigsq)
 !          rij_shift = 1.0D0  / rij - sig + sig0ij
 !          rij_shift = 1.0D0  / rij - sig + sig0ij
-          rij_shift = 1.0/rij - sig + sig0ij
-          IF (rij_shift.le.0.0D0) THEN
-           evdw = 1.0D20
-           RETURN
-          END IF
-          sigder = -sig * sigsq
-          rij_shift = 1.0D0 / rij_shift
-          fac       = rij_shift**expon
-          c1        = fac  * fac * aa_scbase(itypi,itypj)
+        rij_shift = 1.0/rij - sig + sig0ij
+        IF (rij_shift.le.0.0D0) THEN
+         evdw = 1.0D20
+         RETURN
+        END IF
+        sigder = -sig * sigsq
+        rij_shift = 1.0D0 / rij_shift
+        fac       = rij_shift**expon
+        c1        = fac  * fac * aa_scbase(itypi,itypj)
 !          c1        = 0.0d0
 !          c1        = 0.0d0
-          c2        = fac  * bb_scbase(itypi,itypj)
+        c2        = fac  * bb_scbase(itypi,itypj)
 !          c2        = 0.0d0
 !          c2        = 0.0d0
-          evdwij    = eps1 * eps2rt * eps3rt * ( c1 + c2 )
-          eps2der   = eps3rt * evdwij
-          eps3der   = eps2rt * evdwij
+        evdwij    = eps1 * eps2rt * eps3rt * ( c1 + c2 )
+        eps2der   = eps3rt * evdwij
+        eps3der   = eps2rt * evdwij
 !          evdwij    = 4.0d0 * eps2rt * eps3rt * evdwij
 !          evdwij    = 4.0d0 * eps2rt * eps3rt * evdwij
-          evdwij    = eps2rt * eps3rt * evdwij
-          c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
-          fac    = -expon * (c1 + evdwij) * rij_shift
-          sigder = fac * sigder
+        evdwij    = eps2rt * eps3rt * evdwij
+        c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
+        fac    = -expon * (c1 + evdwij) * rij_shift
+        sigder = fac * sigder
 !          fac    = rij * fac
 ! Calculate distance derivative
 !          fac    = rij * fac
 ! Calculate distance derivative
-          gg(1) =  fac
-          gg(2) =  fac
-          gg(3) =  fac
+        gg(1) =  fac
+        gg(2) =  fac
+        gg(3) =  fac
 !          if (b2.gt.0.0) then
 !          if (b2.gt.0.0) then
-          fac = chis1 * sqom1 + chis2 * sqom2 &
-          - 2.0d0 * chis12 * om1 * om2 * om12
+        fac = chis1 * sqom1 + chis2 * sqom2 &
+        - 2.0d0 * chis12 * om1 * om2 * om12
 ! we will use pom later in Gcav, so dont mess with it!
 ! we will use pom later in Gcav, so dont mess with it!
-          pom = 1.0d0 - chis1 * chis2 * sqom12
-          Lambf = (1.0d0 - (fac / pom))
-          Lambf = dsqrt(Lambf)
-          sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
+        pom = 1.0d0 - chis1 * chis2 * sqom12
+        Lambf = (1.0d0 - (fac / pom))
+        Lambf = dsqrt(Lambf)
+        sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
 !       write (*,*) "sparrow = ", sparrow
 !       write (*,*) "sparrow = ", sparrow
-          Chif = 1.0d0/rij * sparrow
-          ChiLambf = Chif * Lambf
-          eagle = dsqrt(ChiLambf)
-          bat = ChiLambf ** 11.0d0
-          top = b1 * ( eagle + b2 * ChiLambf - b3 )
-          bot = 1.0d0 + b4 * (ChiLambf ** 12.0d0)
-          botsq = bot * bot
-          Fcav = top / bot
+        Chif = 1.0d0/rij * sparrow
+        ChiLambf = Chif * Lambf
+        eagle = dsqrt(ChiLambf)
+        bat = ChiLambf ** 11.0d0
+        top = b1 * ( eagle + b2 * ChiLambf - b3 )
+        bot = 1.0d0 + b4 * (ChiLambf ** 12.0d0)
+        botsq = bot * bot
+        Fcav = top / bot
 !          print *,i,j,Fcav
 !          print *,i,j,Fcav
-          dtop = b1 * ((Lambf / (2.0d0 * eagle)) + (b2 * Lambf))
-          dbot = 12.0d0 * b4 * bat * Lambf
-          dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
+        dtop = b1 * ((Lambf / (2.0d0 * eagle)) + (b2 * Lambf))
+        dbot = 12.0d0 * b4 * bat * Lambf
+        dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
 !       dFdR = 0.0d0
 !      write (*,*) "dFcav/dR = ", dFdR
 !       dFdR = 0.0d0
 !      write (*,*) "dFcav/dR = ", dFdR
-          dtop = b1 * ((Chif / (2.0d0 * eagle)) + (b2 * Chif))
-          dbot = 12.0d0 * b4 * bat * Chif
-          eagle = Lambf * pom
-          dFdOM1  = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
-          dFdOM2  = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
-          dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
-              * (chis2 * om2 * om12 - om1) / (eagle * pom)
-
-          dFdL = ((dtop * bot - top * dbot) / botsq)
+        dtop = b1 * ((Chif / (2.0d0 * eagle)) + (b2 * Chif))
+        dbot = 12.0d0 * b4 * bat * Chif
+        eagle = Lambf * pom
+        dFdOM1  = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
+        dFdOM2  = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
+        dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
+            * (chis2 * om2 * om12 - om1) / (eagle * pom)
+
+        dFdL = ((dtop * bot - top * dbot) / botsq)
 !       dFdL = 0.0d0
 !       dFdL = 0.0d0
-          dCAVdOM1  = dFdL * ( dFdOM1 )
-          dCAVdOM2  = dFdL * ( dFdOM2 )
-          dCAVdOM12 = dFdL * ( dFdOM12 )
-          
-          ertail(1) = xj*rij
-          ertail(2) = yj*rij
-          ertail(3) = zj*rij
+        dCAVdOM1  = dFdL * ( dFdOM1 )
+        dCAVdOM2  = dFdL * ( dFdOM2 )
+        dCAVdOM12 = dFdL * ( dFdOM12 )
+        
+        ertail(1) = xj*rij
+        ertail(2) = yj*rij
+        ertail(3) = zj*rij
 !      eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1
 !      eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2
 !      eom12=evdwij*eps1_om12+eps2der*eps2rt_om12 &
 !      eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1
 !      eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2
 !      eom12=evdwij*eps1_om12+eps2der*eps2rt_om12 &
@@ -24022,30 +24032,30 @@
        DO k = 1, 3
 !      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
        DO k = 1, 3
 !      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
-        pom = ertail(k)
+      pom = ertail(k)
 !-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
 !-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
-        gvdwx_scbase(k,i) = gvdwx_scbase(k,i) &
-                  - (( dFdR + gg(k) ) * pom)  
+      gvdwx_scbase(k,i) = gvdwx_scbase(k,i) &
+              - (( dFdR + gg(k) ) * pom)  
 !                 +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
 !                 +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
 !     &             - ( dFdR * pom )
 !                 +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
 !                 +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
 !     &             - ( dFdR * pom )
-        pom = ertail(k)
+      pom = ertail(k)
 !-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres))
 !-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres))
-        gvdwx_scbase(k,j) = gvdwx_scbase(k,j) &
-                  + (( dFdR + gg(k) ) * pom)  
+      gvdwx_scbase(k,j) = gvdwx_scbase(k,j) &
+              + (( dFdR + gg(k) ) * pom)  
 !                 +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
 !                 +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
 !c!     &             + ( dFdR * pom )
 
 !                 +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
 !                 +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
 !c!     &             + ( dFdR * pom )
 
-        gvdwc_scbase(k,i) = gvdwc_scbase(k,i) &
-                  - (( dFdR + gg(k) ) * ertail(k))
+      gvdwc_scbase(k,i) = gvdwc_scbase(k,i) &
+              - (( dFdR + gg(k) ) * ertail(k))
 !c!     &             - ( dFdR * ertail(k))
 
 !c!     &             - ( dFdR * ertail(k))
 
-        gvdwc_scbase(k,j) = gvdwc_scbase(k,j) &
-                  + (( dFdR + gg(k) ) * ertail(k))
+      gvdwc_scbase(k,j) = gvdwc_scbase(k,j) &
+              + (( dFdR + gg(k) ) * ertail(k))
 !c!     &             + ( dFdR * ertail(k))
 
 !c!     &             + ( dFdR * ertail(k))
 
-        gg(k) = 0.0d0
+      gg(k) = 0.0d0
 !c!      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !c!      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
       END DO
 !c!      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !c!      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
       END DO
@@ -24054,7 +24064,7 @@
 
 !          endif
 !Now dipole-dipole
 
 !          endif
 !Now dipole-dipole
-         if (wdipdip_scbase(2,itypi,itypj).gt.0.0d0) then
+       if (wdipdip_scbase(2,itypi,itypj).gt.0.0d0) then
        w1 = wdipdip_scbase(1,itypi,itypj)
        w2 = -wdipdip_scbase(3,itypi,itypj)/2.0
        w3 = wdipdip_scbase(2,itypi,itypj)
        w1 = wdipdip_scbase(1,itypi,itypj)
        w2 = -wdipdip_scbase(3,itypi,itypj)/2.0
        w3 = wdipdip_scbase(2,itypi,itypj)
@@ -24063,9 +24073,9 @@
        fac = (om12 - 3.0d0 * om1 * om2)
        c1 = (w1 / (Rhead**3.0d0)) * fac
        c2 = (w2 / Rhead ** 6.0d0)  &
        fac = (om12 - 3.0d0 * om1 * om2)
        c1 = (w1 / (Rhead**3.0d0)) * fac
        c2 = (w2 / Rhead ** 6.0d0)  &
-         * (4.0d0 + fac * fac -3.0d0 * (sqom1 + sqom2))
+       * (4.0d0 + fac * fac -3.0d0 * (sqom1 + sqom2))
        c3= (w3/ Rhead ** 6.0d0)  &
        c3= (w3/ Rhead ** 6.0d0)  &
-         * (2.0d0 - 2.0d0*fac*fac +3.0d0*(sqom1 + sqom2))
+       * (2.0d0 - 2.0d0*fac*fac +3.0d0*(sqom1 + sqom2))
        ECL = c1 - c2 + c3
 !c!       write (*,*) "w1 = ", w1
 !c!       write (*,*) "w2 = ", w2
        ECL = c1 - c2 + c3
 !c!       write (*,*) "w1 = ", w1
 !c!       write (*,*) "w2 = ", w2
@@ -24084,20 +24094,20 @@
 !c! dECL/dr
        c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
        c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) &
 !c! dECL/dr
        c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
        c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) &
-         * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2))
+       * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2))
        c3=  (-6.0d0 * w3) / (Rhead ** 7.0d0) &
        c3=  (-6.0d0 * w3) / (Rhead ** 7.0d0) &
-         * (2.0d0 - 2.0d0*fac*fac +3.0d0*(sqom1 + sqom2))
+       * (2.0d0 - 2.0d0*fac*fac +3.0d0*(sqom1 + sqom2))
        dGCLdR = c1 - c2 + c3
 !c! dECL/dom1
        c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
        dGCLdR = c1 - c2 + c3
 !c! dECL/dom1
        c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
-         * ( om2 * om12 - 3.0d0 * om1 * sqom2 + om1 )
+       * ( om2 * om12 - 3.0d0 * om1 * sqom2 + om1 )
        c3 =(6.0d0*w3/ Rhead ** 6.0d0)*(om1-2.0d0*(fac)*(-om2))
        dGCLdOM1 = c1 - c2 + c3 
 !c! dECL/dom2
        c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
        c3 =(6.0d0*w3/ Rhead ** 6.0d0)*(om1-2.0d0*(fac)*(-om2))
        dGCLdOM1 = c1 - c2 + c3 
 !c! dECL/dom2
        c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
-         * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 )
+       * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 )
        c3 =(6.0d0*w3/ Rhead ** 6.0d0)*(om2-2.0d0*(fac)*(-om1))
        dGCLdOM2 = c1 - c2 + c3
 !c! dECL/dom12
        c3 =(6.0d0*w3/ Rhead ** 6.0d0)*(om2-2.0d0*(fac)*(-om1))
        dGCLdOM2 = c1 - c2 + c3
 !c! dECL/dom12
@@ -24106,7 +24116,7 @@
        c3 = (w3/ Rhead ** 6.0d0)*(-4.0d0*fac)
        dGCLdOM12 = c1 - c2 + c3
        DO k= 1, 3
        c3 = (w3/ Rhead ** 6.0d0)*(-4.0d0*fac)
        dGCLdOM12 = c1 - c2 + c3
        DO k= 1, 3
-        erhead(k) = Rhead_distance(k)/Rhead
+      erhead(k) = Rhead_distance(k)/Rhead
        END DO
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
        erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
        END DO
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
        erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
@@ -24114,17 +24124,17 @@
        facd2 = d1j * vbld_inv(j+nres)
        DO k = 1, 3
 
        facd2 = d1j * vbld_inv(j+nres)
        DO k = 1, 3
 
-        pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
-        gvdwx_scbase(k,i) = gvdwx_scbase(k,i) &
-                  - dGCLdR * pom
-        pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
-        gvdwx_scbase(k,j) = gvdwx_scbase(k,j) &
-                  + dGCLdR * pom
-
-        gvdwc_scbase(k,i) = gvdwc_scbase(k,i) &
-                  - dGCLdR * erhead(k)
-        gvdwc_scbase(k,j) = gvdwc_scbase(k,j) &
-                  + dGCLdR * erhead(k)
+      pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+      gvdwx_scbase(k,i) = gvdwx_scbase(k,i) &
+              - dGCLdR * pom
+      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+      gvdwx_scbase(k,j) = gvdwx_scbase(k,j) &
+              + dGCLdR * pom
+
+      gvdwc_scbase(k,i) = gvdwc_scbase(k,i) &
+              - dGCLdR * erhead(k)
+      gvdwc_scbase(k,j) = gvdwc_scbase(k,j) &
+              + dGCLdR * erhead(k)
        END DO
        endif
 !now charge with dipole eg. ARG-dG
        END DO
        endif
 !now charge with dipole eg. ARG-dG
@@ -24141,7 +24151,7 @@
        R1 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances tail is center of side-chain
        R1 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances tail is center of side-chain
-        R1=R1+(c(k,j+nres)-chead(k,1))**2
+      R1=R1+(c(k,j+nres)-chead(k,1))**2
        END DO
 !c! Pitagoras
        R1 = dsqrt(R1)
        END DO
 !c! Pitagoras
        R1 = dsqrt(R1)
@@ -24156,12 +24166,12 @@
        sparrow  = w1  *  om1
        hawk     = w2 *  (1.0d0 - sqom2)
        Ecl = sparrow / Rhead**2.0d0 &
        sparrow  = w1  *  om1
        hawk     = w2 *  (1.0d0 - sqom2)
        Ecl = sparrow / Rhead**2.0d0 &
-           - hawk    / Rhead**4.0d0
+         - hawk    / Rhead**4.0d0
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part
        dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part
        dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
-                + 4.0d0 * hawk    / Rhead**5.0d0
+            + 4.0d0 * hawk    / Rhead**5.0d0
 !c! dF/dom1
        dGCLdOM1 = (w1) / (Rhead**2.0d0)
 !c! dF/dom2
 !c! dF/dom1
        dGCLdOM1 = (w1) / (Rhead**2.0d0)
 !c! dF/dom2
@@ -24177,20 +24187,20 @@
        epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0)
 ! derivative of Epol is Gpol...
        dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0) &
        epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0)
 ! derivative of Epol is Gpol...
        dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0) &
-                / (fgb1 ** 5.0d0)
+            / (fgb1 ** 5.0d0)
        dFGBdR1 = ( (R1 / MomoFac1) &
        dFGBdR1 = ( (R1 / MomoFac1) &
-             * ( 2.0d0 - (0.5d0 * ee1) ) ) &
-             / ( 2.0d0 * fgb1 )
+           * ( 2.0d0 - (0.5d0 * ee1) ) ) &
+           / ( 2.0d0 * fgb1 )
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
-               * (2.0d0 - 0.5d0 * ee1) ) &
-               / (2.0d0 * fgb1)
+             * (2.0d0 - 0.5d0 * ee1) ) &
+             / (2.0d0 * fgb1)
        dPOLdR1 = dPOLdFGB1 * dFGBdR1
 !       dPOLdR1 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
        DO k = 1, 3
        dPOLdR1 = dPOLdFGB1 * dFGBdR1
 !       dPOLdR1 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
        DO k = 1, 3
-        erhead(k) = Rhead_distance(k)/Rhead
-        erhead_tail(k,1) = ((c(k,j+nres)-chead(k,1))/R1)
+      erhead(k) = Rhead_distance(k)/Rhead
+      erhead_tail(k,1) = ((c(k,j+nres)-chead(k,1))/R1)
        END DO
 
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
        END DO
 
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
@@ -24203,31 +24213,31 @@
 !       facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
 
        DO k = 1, 3
 !       facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
 
        DO k = 1, 3
-        hawk = (erhead_tail(k,1) + &
-        facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
+      hawk = (erhead_tail(k,1) + &
+      facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
 !        facd1=0.0d0
 !        facd2=0.0d0
 !        facd1=0.0d0
 !        facd2=0.0d0
-        pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
-        gvdwx_scbase(k,i) = gvdwx_scbase(k,i)   &
-                   - dGCLdR * pom &
-                   - dPOLdR1 *  (erhead_tail(k,1))
+      pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+      gvdwx_scbase(k,i) = gvdwx_scbase(k,i)   &
+               - dGCLdR * pom &
+               - dPOLdR1 *  (erhead_tail(k,1))
 !     &             - dGLJdR * pom
 
 !     &             - dGLJdR * pom
 
-        pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
-        gvdwx_scbase(k,j) = gvdwx_scbase(k,j)    &
-                   + dGCLdR * pom  &
-                   + dPOLdR1 * (erhead_tail(k,1))
+      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+      gvdwx_scbase(k,j) = gvdwx_scbase(k,j)    &
+               + dGCLdR * pom  &
+               + dPOLdR1 * (erhead_tail(k,1))
 !     &             + dGLJdR * pom
 
 
 !     &             + dGLJdR * pom
 
 
-        gvdwc_scbase(k,i) = gvdwc_scbase(k,i)  &
-                  - dGCLdR * erhead(k) &
-                  - dPOLdR1 * erhead_tail(k,1)
+      gvdwc_scbase(k,i) = gvdwc_scbase(k,i)  &
+              - dGCLdR * erhead(k) &
+              - dPOLdR1 * erhead_tail(k,1)
 !     &             - dGLJdR * erhead(k)
 
 !     &             - dGLJdR * erhead(k)
 
-        gvdwc_scbase(k,j) = gvdwc_scbase(k,j)         &
-                  + dGCLdR * erhead(k)  &
-                  + dPOLdR1 * erhead_tail(k,1)
+      gvdwc_scbase(k,j) = gvdwc_scbase(k,j)         &
+              + dGCLdR * erhead(k)  &
+              + dPOLdR1 * erhead_tail(k,1)
 !     &             + dGLJdR * erhead(k)
 
        END DO
 !     &             + dGLJdR * erhead(k)
 
        END DO
@@ -24235,7 +24245,7 @@
 !       print *,i,j,evdwij,epol,Fcav,ECL
        escbase=escbase+evdwij+epol+Fcav+ECL
        call sc_grad_scbase
 !       print *,i,j,evdwij,epol,Fcav,ECL
        escbase=escbase+evdwij+epol+Fcav+ECL
        call sc_grad_scbase
-         enddo
+       enddo
       enddo
 
       return
       enddo
 
       return
@@ -24245,44 +24255,44 @@
 
        real (kind=8) :: dcosom1(3),dcosom2(3)
        eom1  =    &
 
        real (kind=8) :: dcosom1(3),dcosom2(3)
        eom1  =    &
-              eps2der * eps2rt_om1   &
-            - 2.0D0 * alf1 * eps3der &
-            + sigder * sigsq_om1     &
-            + dCAVdOM1               &
-            + dGCLdOM1               &
-            + dPOLdOM1
+            eps2der * eps2rt_om1   &
+          - 2.0D0 * alf1 * eps3der &
+          + sigder * sigsq_om1     &
+          + dCAVdOM1               &
+          + dGCLdOM1               &
+          + dPOLdOM1
 
        eom2  =  &
 
        eom2  =  &
-              eps2der * eps2rt_om2   &
-            + 2.0D0 * alf2 * eps3der &
-            + sigder * sigsq_om2     &
-            + dCAVdOM2               &
-            + dGCLdOM2               &
-            + dPOLdOM2
+            eps2der * eps2rt_om2   &
+          + 2.0D0 * alf2 * eps3der &
+          + sigder * sigsq_om2     &
+          + dCAVdOM2               &
+          + dGCLdOM2               &
+          + dPOLdOM2
 
        eom12 =    &
 
        eom12 =    &
-              evdwij  * eps1_om12     &
-            + eps2der * eps2rt_om12   &
-            - 2.0D0 * alf12 * eps3der &
-            + sigder *sigsq_om12      &
-            + dCAVdOM12               &
-            + dGCLdOM12
+            evdwij  * eps1_om12     &
+          + eps2der * eps2rt_om12   &
+          - 2.0D0 * alf12 * eps3der &
+          + sigder *sigsq_om12      &
+          + dCAVdOM12               &
+          + dGCLdOM12
 
 !       print *,eom1,eom2,eom12,i,j,"eom1,2,12",erij(1),erij(2),erij(3)
 !       print *,dsci_inv,dscj_inv,dc_norm(2,nres+j),dc_norm(2,nres+i),&
 !               gg(1),gg(2),"rozne"
        DO k = 1, 3
 
 !       print *,eom1,eom2,eom12,i,j,"eom1,2,12",erij(1),erij(2),erij(3)
 !       print *,dsci_inv,dscj_inv,dc_norm(2,nres+j),dc_norm(2,nres+i),&
 !               gg(1),gg(2),"rozne"
        DO k = 1, 3
-        dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k))
-        dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
-        gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
-        gvdwx_scbase(k,i)= gvdwx_scbase(k,i) - gg(k)   &
-                 + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
-                 + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
-        gvdwx_scbase(k,j)= gvdwx_scbase(k,j) + gg(k)  &
-                 + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
-                 + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
-        gvdwc_scbase(k,i)=gvdwc_scbase(k,i)-gg(k)
-        gvdwc_scbase(k,j)=gvdwc_scbase(k,j)+gg(k)
+      dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k))
+      dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
+      gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
+      gvdwx_scbase(k,i)= gvdwx_scbase(k,i) - gg(k)   &
+             + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
+             + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+      gvdwx_scbase(k,j)= gvdwx_scbase(k,j) + gg(k)  &
+             + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
+             + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+      gvdwc_scbase(k,i)=gvdwc_scbase(k,i)-gg(k)
+      gvdwc_scbase(k,j)=gvdwc_scbase(k,j)+gg(k)
        END DO
        RETURN
       END SUBROUTINE sc_grad_scbase
        END DO
        RETURN
       END SUBROUTINE sc_grad_scbase
@@ -24296,144 +24306,106 @@
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
       real(kind=8) :: evdw,sig0ij
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
       real(kind=8) :: evdw,sig0ij
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
-                    dist_temp, dist_init,aa,bb,ssgradlipi,ssgradlipj, &
-                    sslipi,sslipj,faclip
+                dist_temp, dist_init,aa,bb,ssgradlipi,ssgradlipj, &
+                sslipi,sslipj,faclip
       integer :: ii
       real(kind=8) :: fracinbuf
        real (kind=8) :: epepbase
        real (kind=8),dimension(4):: ener
        real(kind=8) :: b1,b2,b3,b4,egb,eps_in,eps_inout_fac,eps_out
        real(kind=8) :: ECL,Elj,Equad,Epol,eheadtail,rhead,dGCLOM2,&
       integer :: ii
       real(kind=8) :: fracinbuf
        real (kind=8) :: epepbase
        real (kind=8),dimension(4):: ener
        real(kind=8) :: b1,b2,b3,b4,egb,eps_in,eps_inout_fac,eps_out
        real(kind=8) :: ECL,Elj,Equad,Epol,eheadtail,rhead,dGCLOM2,&
-        sqom1,sqom2,sqom12,c1,c2,c3,pom,Lambf,sparrow,&
-        Chif,ChiLambf,bat,eagle,top,bot,botsq,Fcav,dtop,dFdR,dFdOM1,&
-        dFdOM2,w1,w2,w3,dGCLdR,dFdL,dFdOM12,dbot ,&
-        r1,eps_head,alphapol1,pis,facd2,d2,facd1,d1,erdxj,erdxi,federmaus,&
-        dPOLdR1,dFGBdOM2,dFGBdR1,dPOLdFGB1,RR1,MomoFac1,hawk,d1i,d1j,&
-        sig1,sig2,chis12,chis2,ee1,fgb1,a12sq,chis1
+      sqom1,sqom2,sqom12,c1,c2,c3,pom,Lambf,sparrow,&
+      Chif,ChiLambf,bat,eagle,top,bot,botsq,Fcav,dtop,dFdR,dFdOM1,&
+      dFdOM2,w1,w2,w3,dGCLdR,dFdL,dFdOM12,dbot ,&
+      r1,eps_head,alphapol1,pis,facd2,d2,facd1,d1,erdxj,erdxi,federmaus,&
+      dPOLdR1,dFGBdOM2,dFGBdR1,dPOLdFGB1,RR1,MomoFac1,hawk,d1i,d1j,&
+      sig1,sig2,chis12,chis2,ee1,fgb1,a12sq,chis1
        real(kind=8),dimension(3,2)::chead,erhead_tail
        real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead
        integer troll
        eps_out=80.0d0
        epepbase=0.0d0
 !       do i=1,nres_molec(1)-1
        real(kind=8),dimension(3,2)::chead,erhead_tail
        real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead
        integer troll
        eps_out=80.0d0
        epepbase=0.0d0
 !       do i=1,nres_molec(1)-1
-        do i=ibond_start,ibond_end
-        if (itype(i,1).eq.ntyp1_molec(1).or.itype(i+1,1).eq.ntyp1_molec(1)) cycle
+      do i=ibond_start,ibond_end
+      if (itype(i,1).eq.ntyp1_molec(1).or.itype(i+1,1).eq.ntyp1_molec(1)) cycle
 !C        itypi  = itype(i,1)
 !C        itypi  = itype(i,1)
-        dxi    = dc_norm(1,i)
-        dyi    = dc_norm(2,i)
-        dzi    = dc_norm(3,i)
+      dxi    = dc_norm(1,i)
+      dyi    = dc_norm(2,i)
+      dzi    = dc_norm(3,i)
 !        print *,dxi,(-c(1,i)+c(1,i+1))*vbld_inv(i+1)
 !        print *,dxi,(-c(1,i)+c(1,i+1))*vbld_inv(i+1)
-        dsci_inv = vbld_inv(i+1)/2.0
-        xi=(c(1,i)+c(1,i+1))/2.0
-        yi=(c(2,i)+c(2,i+1))/2.0
-        zi=(c(3,i)+c(3,i+1))/2.0
-        xi=mod(xi,boxxsize)
-         if (xi.lt.0) xi=xi+boxxsize
-        yi=mod(yi,boxysize)
-         if (yi.lt.0) yi=yi+boxysize
-        zi=mod(zi,boxzsize)
-         if (zi.lt.0) zi=zi+boxzsize
-         do j=nres_molec(1)+1,nres_molec(2)+nres_molec(1)
-           itypj= itype(j,2)
-           if (itype(j,2).eq.ntyp1_molec(2))cycle
-           xj=c(1,j+nres)
-           yj=c(2,j+nres)
-           zj=c(3,j+nres)
-           xj=dmod(xj,boxxsize)
-           if (xj.lt.0) xj=xj+boxxsize
-           yj=dmod(yj,boxysize)
-           if (yj.lt.0) yj=yj+boxysize
-           zj=dmod(zj,boxzsize)
-           if (zj.lt.0) zj=zj+boxzsize
-          dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          xj_safe=xj
-          yj_safe=yj
-          zj_safe=zj
-          subchap=0
-
-          do xshift=-1,1
-          do yshift=-1,1
-          do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-          enddo
-          enddo
-          enddo
-          if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-          else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-          endif
-          dxj = dc_norm( 1, nres+j )
-          dyj = dc_norm( 2, nres+j )
-          dzj = dc_norm( 3, nres+j )
+      dsci_inv = vbld_inv(i+1)/2.0
+      xi=(c(1,i)+c(1,i+1))/2.0
+      yi=(c(2,i)+c(2,i+1))/2.0
+      zi=(c(3,i)+c(3,i+1))/2.0
+        call to_box(xi,yi,zi)       
+       do j=nres_molec(1)+1,nres_molec(2)+nres_molec(1)
+         itypj= itype(j,2)
+         if (itype(j,2).eq.ntyp1_molec(2))cycle
+         xj=c(1,j+nres)
+         yj=c(2,j+nres)
+         zj=c(3,j+nres)
+                call to_box(xj,yj,zj)
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)
+        dist_init=xj**2+yj**2+zj**2
+        dxj = dc_norm( 1, nres+j )
+        dyj = dc_norm( 2, nres+j )
+        dzj = dc_norm( 3, nres+j )
 !          d1i = dhead_scbasei(itypi) !this is shift of dipole/charge
 !          d1j = dhead_scbasej(itypi) !this is shift of dipole/charge
 
 ! Gay-berne var's
 !          d1i = dhead_scbasei(itypi) !this is shift of dipole/charge
 !          d1j = dhead_scbasej(itypi) !this is shift of dipole/charge
 
 ! Gay-berne var's
-          sig0ij = sigma_pepbase(itypj )
-          chi1   = chi_pepbase(itypj,1 )
-          chi2   = chi_pepbase(itypj,2 )
+        sig0ij = sigma_pepbase(itypj )
+        chi1   = chi_pepbase(itypj,1 )
+        chi2   = chi_pepbase(itypj,2 )
 !          chi1=0.0d0
 !          chi2=0.0d0
 !          chi1=0.0d0
 !          chi2=0.0d0
-          chi12  = chi1 * chi2
-          chip1  = chipp_pepbase(itypj,1 )
-          chip2  = chipp_pepbase(itypj,2 )
+        chi12  = chi1 * chi2
+        chip1  = chipp_pepbase(itypj,1 )
+        chip2  = chipp_pepbase(itypj,2 )
 !          chip1=0.0d0
 !          chip2=0.0d0
 !          chip1=0.0d0
 !          chip2=0.0d0
-          chip12 = chip1 * chip2
-          chis1 = chis_pepbase(itypj,1)
-          chis2 = chis_pepbase(itypj,2)
-          chis12 = chis1 * chis2
-          sig1 = sigmap1_pepbase(itypj)
-          sig2 = sigmap2_pepbase(itypj)
+        chip12 = chip1 * chip2
+        chis1 = chis_pepbase(itypj,1)
+        chis2 = chis_pepbase(itypj,2)
+        chis12 = chis1 * chis2
+        sig1 = sigmap1_pepbase(itypj)
+        sig2 = sigmap2_pepbase(itypj)
 !       write (*,*) "sig1 = ", sig1
 !       write (*,*) "sig2 = ", sig2
        DO k = 1,3
 ! location of polar head is computed by taking hydrophobic centre
 ! and moving by a d1 * dc_norm vector
 ! see unres publications for very informative images
 !       write (*,*) "sig1 = ", sig1
 !       write (*,*) "sig2 = ", sig2
        DO k = 1,3
 ! location of polar head is computed by taking hydrophobic centre
 ! and moving by a d1 * dc_norm vector
 ! see unres publications for very informative images
-        chead(k,1) = (c(k,i)+c(k,i+1))/2.0
+      chead(k,1) = (c(k,i)+c(k,i+1))/2.0
 ! + d1i * dc_norm(k, i+nres)
 ! + d1i * dc_norm(k, i+nres)
-        chead(k,2) = c(k, j+nres)
+      chead(k,2) = c(k, j+nres)
 ! + d1j * dc_norm(k, j+nres)
 ! distance 
 !        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
 !        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
 ! + d1j * dc_norm(k, j+nres)
 ! distance 
 !        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
 !        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
-        Rhead_distance(k) = chead(k,2) - chead(k,1)
+      Rhead_distance(k) = chead(k,2) - chead(k,1)
 !        print *,gvdwc_pepbase(k,i)
 
        END DO
        Rhead = dsqrt( &
 !        print *,gvdwc_pepbase(k,i)
 
        END DO
        Rhead = dsqrt( &
-          (Rhead_distance(1)*Rhead_distance(1)) &
-        + (Rhead_distance(2)*Rhead_distance(2)) &
-        + (Rhead_distance(3)*Rhead_distance(3)))
+        (Rhead_distance(1)*Rhead_distance(1)) &
+      + (Rhead_distance(2)*Rhead_distance(2)) &
+      + (Rhead_distance(3)*Rhead_distance(3)))
 
 ! alpha factors from Fcav/Gcav
 
 ! alpha factors from Fcav/Gcav
-          b1 = alphasur_pepbase(1,itypj)
+        b1 = alphasur_pepbase(1,itypj)
 !          b1=0.0d0
 !          b1=0.0d0
-          b2 = alphasur_pepbase(2,itypj)
-          b3 = alphasur_pepbase(3,itypj)
-          b4 = alphasur_pepbase(4,itypj)
-          alf1   = 0.0d0
-          alf2   = 0.0d0
-          alf12  = 0.0d0
-          rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
+        b2 = alphasur_pepbase(2,itypj)
+        b3 = alphasur_pepbase(3,itypj)
+        b4 = alphasur_pepbase(4,itypj)
+        alf1   = 0.0d0
+        alf2   = 0.0d0
+        alf12  = 0.0d0
+        rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
 !          print *,i,j,rrij
 !          print *,i,j,rrij
-          rij  = dsqrt(rrij)
+        rij  = dsqrt(rrij)
 !----------------------------
        evdwij = 0.0d0
        ECL = 0.0d0
 !----------------------------
        evdwij = 0.0d0
        ECL = 0.0d0
@@ -24447,118 +24419,118 @@
        dGCLdOM12 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0
        dGCLdOM12 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0
-          Fcav = 0.0d0
-          dFdR = 0.0d0
-          dCAVdOM1  = 0.0d0
-          dCAVdOM2  = 0.0d0
-          dCAVdOM12 = 0.0d0
-          dscj_inv = vbld_inv(j+nres)
-          CALL sc_angular
+        Fcav = 0.0d0
+        dFdR = 0.0d0
+        dCAVdOM1  = 0.0d0
+        dCAVdOM2  = 0.0d0
+        dCAVdOM12 = 0.0d0
+        dscj_inv = vbld_inv(j+nres)
+        CALL sc_angular
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials
 ! om = omega, sqom = om^2
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials
 ! om = omega, sqom = om^2
-          sqom1  = om1 * om1
-          sqom2  = om2 * om2
-          sqom12 = om12 * om12
+        sqom1  = om1 * om1
+        sqom2  = om2 * om2
+        sqom12 = om12 * om12
 
 ! now we calculate EGB - Gey-Berne
 ! It will be summed up in evdwij and saved in evdw
 
 ! now we calculate EGB - Gey-Berne
 ! It will be summed up in evdwij and saved in evdw
-          sigsq     = 1.0D0  / sigsq
-          sig       = sig0ij * dsqrt(sigsq)
-          rij_shift = 1.0/rij - sig + sig0ij
-          IF (rij_shift.le.0.0D0) THEN
-           evdw = 1.0D20
-           RETURN
-          END IF
-          sigder = -sig * sigsq
-          rij_shift = 1.0D0 / rij_shift
-          fac       = rij_shift**expon
-          c1        = fac  * fac * aa_pepbase(itypj)
+        sigsq     = 1.0D0  / sigsq
+        sig       = sig0ij * dsqrt(sigsq)
+        rij_shift = 1.0/rij - sig + sig0ij
+        IF (rij_shift.le.0.0D0) THEN
+         evdw = 1.0D20
+         RETURN
+        END IF
+        sigder = -sig * sigsq
+        rij_shift = 1.0D0 / rij_shift
+        fac       = rij_shift**expon
+        c1        = fac  * fac * aa_pepbase(itypj)
 !          c1        = 0.0d0
 !          c1        = 0.0d0
-          c2        = fac  * bb_pepbase(itypj)
+        c2        = fac  * bb_pepbase(itypj)
 !          c2        = 0.0d0
 !          c2        = 0.0d0
-          evdwij    = eps1 * eps2rt * eps3rt * ( c1 + c2 )
-          eps2der   = eps3rt * evdwij
-          eps3der   = eps2rt * evdwij
+        evdwij    = eps1 * eps2rt * eps3rt * ( c1 + c2 )
+        eps2der   = eps3rt * evdwij
+        eps3der   = eps2rt * evdwij
 !          evdwij    = 4.0d0 * eps2rt * eps3rt * evdwij
 !          evdwij    = 4.0d0 * eps2rt * eps3rt * evdwij
-          evdwij    = eps2rt * eps3rt * evdwij
-          c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
-          fac    = -expon * (c1 + evdwij) * rij_shift
-          sigder = fac * sigder
+        evdwij    = eps2rt * eps3rt * evdwij
+        c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
+        fac    = -expon * (c1 + evdwij) * rij_shift
+        sigder = fac * sigder
 !          fac    = rij * fac
 ! Calculate distance derivative
 !          fac    = rij * fac
 ! Calculate distance derivative
-          gg(1) =  fac
-          gg(2) =  fac
-          gg(3) =  fac
-          fac = chis1 * sqom1 + chis2 * sqom2 &
-          - 2.0d0 * chis12 * om1 * om2 * om12
+        gg(1) =  fac
+        gg(2) =  fac
+        gg(3) =  fac
+        fac = chis1 * sqom1 + chis2 * sqom2 &
+        - 2.0d0 * chis12 * om1 * om2 * om12
 ! we will use pom later in Gcav, so dont mess with it!
 ! we will use pom later in Gcav, so dont mess with it!
-          pom = 1.0d0 - chis1 * chis2 * sqom12
-          Lambf = (1.0d0 - (fac / pom))
-          Lambf = dsqrt(Lambf)
-          sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
+        pom = 1.0d0 - chis1 * chis2 * sqom12
+        Lambf = (1.0d0 - (fac / pom))
+        Lambf = dsqrt(Lambf)
+        sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
 !       write (*,*) "sparrow = ", sparrow
 !       write (*,*) "sparrow = ", sparrow
-          Chif = 1.0d0/rij * sparrow
-          ChiLambf = Chif * Lambf
-          eagle = dsqrt(ChiLambf)
-          bat = ChiLambf ** 11.0d0
-          top = b1 * ( eagle + b2 * ChiLambf - b3 )
-          bot = 1.0d0 + b4 * (ChiLambf ** 12.0d0)
-          botsq = bot * bot
-          Fcav = top / bot
+        Chif = 1.0d0/rij * sparrow
+        ChiLambf = Chif * Lambf
+        eagle = dsqrt(ChiLambf)
+        bat = ChiLambf ** 11.0d0
+        top = b1 * ( eagle + b2 * ChiLambf - b3 )
+        bot = 1.0d0 + b4 * (ChiLambf ** 12.0d0)
+        botsq = bot * bot
+        Fcav = top / bot
 !          print *,i,j,Fcav
 !          print *,i,j,Fcav
-          dtop = b1 * ((Lambf / (2.0d0 * eagle)) + (b2 * Lambf))
-          dbot = 12.0d0 * b4 * bat * Lambf
-          dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
+        dtop = b1 * ((Lambf / (2.0d0 * eagle)) + (b2 * Lambf))
+        dbot = 12.0d0 * b4 * bat * Lambf
+        dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
 !       dFdR = 0.0d0
 !      write (*,*) "dFcav/dR = ", dFdR
 !       dFdR = 0.0d0
 !      write (*,*) "dFcav/dR = ", dFdR
-          dtop = b1 * ((Chif / (2.0d0 * eagle)) + (b2 * Chif))
-          dbot = 12.0d0 * b4 * bat * Chif
-          eagle = Lambf * pom
-          dFdOM1  = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
-          dFdOM2  = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
-          dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
-              * (chis2 * om2 * om12 - om1) / (eagle * pom)
-
-          dFdL = ((dtop * bot - top * dbot) / botsq)
+        dtop = b1 * ((Chif / (2.0d0 * eagle)) + (b2 * Chif))
+        dbot = 12.0d0 * b4 * bat * Chif
+        eagle = Lambf * pom
+        dFdOM1  = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
+        dFdOM2  = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
+        dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
+            * (chis2 * om2 * om12 - om1) / (eagle * pom)
+
+        dFdL = ((dtop * bot - top * dbot) / botsq)
 !       dFdL = 0.0d0
 !       dFdL = 0.0d0
-          dCAVdOM1  = dFdL * ( dFdOM1 )
-          dCAVdOM2  = dFdL * ( dFdOM2 )
-          dCAVdOM12 = dFdL * ( dFdOM12 )
+        dCAVdOM1  = dFdL * ( dFdOM1 )
+        dCAVdOM2  = dFdL * ( dFdOM2 )
+        dCAVdOM12 = dFdL * ( dFdOM12 )
 
 
-          ertail(1) = xj*rij
-          ertail(2) = yj*rij
-          ertail(3) = zj*rij
+        ertail(1) = xj*rij
+        ertail(2) = yj*rij
+        ertail(3) = zj*rij
        DO k = 1, 3
 !      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
        DO k = 1, 3
 !      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
-        pom = ertail(k)
+      pom = ertail(k)
 !-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
 !-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
-        gvdwc_pepbase(k,i) = gvdwc_pepbase(k,i) &
-                  - (( dFdR + gg(k) ) * pom)/2.0
+      gvdwc_pepbase(k,i) = gvdwc_pepbase(k,i) &
+              - (( dFdR + gg(k) ) * pom)/2.0
 !        print *,gvdwc_pepbase(k,i),i,(( dFdR + gg(k) ) * pom)/2.0
 !                 +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
 !                 +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
 !     &             - ( dFdR * pom )
 !        print *,gvdwc_pepbase(k,i),i,(( dFdR + gg(k) ) * pom)/2.0
 !                 +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
 !                 +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
 !     &             - ( dFdR * pom )
-        pom = ertail(k)
+      pom = ertail(k)
 !-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres))
 !-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres))
-        gvdwx_pepbase(k,j) = gvdwx_pepbase(k,j) &
-                  + (( dFdR + gg(k) ) * pom)
+      gvdwx_pepbase(k,j) = gvdwx_pepbase(k,j) &
+              + (( dFdR + gg(k) ) * pom)
 !                 +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
 !                 +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
 !c!     &             + ( dFdR * pom )
 
 !                 +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
 !                 +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
 !c!     &             + ( dFdR * pom )
 
-        gvdwc_pepbase(k,i+1) = gvdwc_pepbase(k,i+1) &
-                  - (( dFdR + gg(k) ) * ertail(k))/2.0
+      gvdwc_pepbase(k,i+1) = gvdwc_pepbase(k,i+1) &
+              - (( dFdR + gg(k) ) * ertail(k))/2.0
 !        print *,gvdwc_pepbase(k,i+1),i+1,(( dFdR + gg(k) ) * pom)/2.0
 
 !c!     &             - ( dFdR * ertail(k))
 
 !        print *,gvdwc_pepbase(k,i+1),i+1,(( dFdR + gg(k) ) * pom)/2.0
 
 !c!     &             - ( dFdR * ertail(k))
 
-        gvdwc_pepbase(k,j) = gvdwc_pepbase(k,j) &
-                  + (( dFdR + gg(k) ) * ertail(k))
+      gvdwc_pepbase(k,j) = gvdwc_pepbase(k,j) &
+              + (( dFdR + gg(k) ) * ertail(k))
 !c!     &             + ( dFdR * ertail(k))
 
 !c!     &             + ( dFdR * ertail(k))
 
-        gg(k) = 0.0d0
+      gg(k) = 0.0d0
 !c!      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !c!      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
       END DO
 !c!      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !c!      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
       END DO
@@ -24575,29 +24547,29 @@
        fac = (om12 - 3.0d0 * om1 * om2)
        c1 = (w1 / (Rhead**3.0d0)) * fac
        c2 = (w2 / Rhead ** 6.0d0)  &
        fac = (om12 - 3.0d0 * om1 * om2)
        c1 = (w1 / (Rhead**3.0d0)) * fac
        c2 = (w2 / Rhead ** 6.0d0)  &
-         * (4.0d0 + fac * fac -3.0d0 * (sqom1 + sqom2))
+       * (4.0d0 + fac * fac -3.0d0 * (sqom1 + sqom2))
        c3= (w3/ Rhead ** 6.0d0)  &
        c3= (w3/ Rhead ** 6.0d0)  &
-         * (2.0d0 - 2.0d0*fac*fac +3.0d0*(sqom1 + sqom2))
+       * (2.0d0 - 2.0d0*fac*fac +3.0d0*(sqom1 + sqom2))
 
        ECL = c1 - c2 + c3 
 
        c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
        c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) &
 
        ECL = c1 - c2 + c3 
 
        c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
        c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) &
-         * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2))
+       * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2))
        c3=  (-6.0d0 * w3) / (Rhead ** 7.0d0) &
        c3=  (-6.0d0 * w3) / (Rhead ** 7.0d0) &
-         * (2.0d0 - 2.0d0*fac*fac +3.0d0*(sqom1 + sqom2))
+       * (2.0d0 - 2.0d0*fac*fac +3.0d0*(sqom1 + sqom2))
 
        dGCLdR = c1 - c2 + c3
 !c! dECL/dom1
        c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
 
        dGCLdR = c1 - c2 + c3
 !c! dECL/dom1
        c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
-         * ( om2 * om12 - 3.0d0 * om1 * sqom2 + om1 )
+       * ( om2 * om12 - 3.0d0 * om1 * sqom2 + om1 )
        c3 =(6.0d0*w3/ Rhead ** 6.0d0)*(om1-2.0d0*(fac)*(-om2))
        dGCLdOM1 = c1 - c2 + c3 
 !c! dECL/dom2
        c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
        c3 =(6.0d0*w3/ Rhead ** 6.0d0)*(om1-2.0d0*(fac)*(-om2))
        dGCLdOM1 = c1 - c2 + c3 
 !c! dECL/dom2
        c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
-         * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 )
+       * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 )
        c3 =(6.0d0*w3/ Rhead ** 6.0d0)*(om2-2.0d0*(fac)*(-om1))
 
        dGCLdOM2 = c1 - c2 + c3 
        c3 =(6.0d0*w3/ Rhead ** 6.0d0)*(om2-2.0d0*(fac)*(-om1))
 
        dGCLdOM2 = c1 - c2 + c3 
@@ -24607,7 +24579,7 @@
        c3 = (w3/ Rhead ** 6.0d0)*(-4.0d0*fac)
        dGCLdOM12 = c1 - c2 + c3
        DO k= 1, 3
        c3 = (w3/ Rhead ** 6.0d0)*(-4.0d0*fac)
        dGCLdOM12 = c1 - c2 + c3
        DO k= 1, 3
-        erhead(k) = Rhead_distance(k)/Rhead
+      erhead(k) = Rhead_distance(k)/Rhead
        END DO
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
        erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
        END DO
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
        erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
@@ -24619,19 +24591,19 @@
 !+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
 !        gvdwx_pepbase(k,i) = gvdwx_scbase(k,i) &
 !                  - dGCLdR * pom
 !+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
 !        gvdwx_pepbase(k,i) = gvdwx_scbase(k,i) &
 !                  - dGCLdR * pom
-        pom = erhead(k)
+      pom = erhead(k)
 !+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
 !+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
-        gvdwx_pepbase(k,j) = gvdwx_pepbase(k,j) &
-                  + dGCLdR * pom
+      gvdwx_pepbase(k,j) = gvdwx_pepbase(k,j) &
+              + dGCLdR * pom
 
 
-        gvdwc_pepbase(k,i) = gvdwc_pepbase(k,i) &
-                  - dGCLdR * erhead(k)/2.0d0
+      gvdwc_pepbase(k,i) = gvdwc_pepbase(k,i) &
+              - dGCLdR * erhead(k)/2.0d0
 !        print *,gvdwc_pepbase(k,i+1),i+1,- dGCLdR * erhead(k)/2.0d0
 !        print *,gvdwc_pepbase(k,i+1),i+1,- dGCLdR * erhead(k)/2.0d0
-        gvdwc_pepbase(k,i+1) = gvdwc_pepbase(k,i+1) &
-                  - dGCLdR * erhead(k)/2.0d0
+      gvdwc_pepbase(k,i+1) = gvdwc_pepbase(k,i+1) &
+              - dGCLdR * erhead(k)/2.0d0
 !        print *,gvdwc_pepbase(k,i+1),i+1,- dGCLdR * erhead(k)/2.0d0
 !        print *,gvdwc_pepbase(k,i+1),i+1,- dGCLdR * erhead(k)/2.0d0
-        gvdwc_pepbase(k,j) = gvdwc_pepbase(k,j) &
-                  + dGCLdR * erhead(k)
+      gvdwc_pepbase(k,j) = gvdwc_pepbase(k,j) &
+              + dGCLdR * erhead(k)
        END DO
 !       print *,i,j,evdwij,Fcav,ECL,"vdw,cav,ecl"
        epepbase=epepbase+evdwij+Fcav+ECL
        END DO
 !       print *,i,j,evdwij,Fcav,ECL,"vdw,cav,ecl"
        epepbase=epepbase+evdwij+Fcav+ECL
@@ -24644,28 +24616,28 @@
 
        real (kind=8) :: dcosom1(3),dcosom2(3)
        eom1  =    &
 
        real (kind=8) :: dcosom1(3),dcosom2(3)
        eom1  =    &
-              eps2der * eps2rt_om1   &
-            - 2.0D0 * alf1 * eps3der &
-            + sigder * sigsq_om1     &
-            + dCAVdOM1               &
-            + dGCLdOM1               &
-            + dPOLdOM1
+            eps2der * eps2rt_om1   &
+          - 2.0D0 * alf1 * eps3der &
+          + sigder * sigsq_om1     &
+          + dCAVdOM1               &
+          + dGCLdOM1               &
+          + dPOLdOM1
 
        eom2  =  &
 
        eom2  =  &
-              eps2der * eps2rt_om2   &
-            + 2.0D0 * alf2 * eps3der &
-            + sigder * sigsq_om2     &
-            + dCAVdOM2               &
-            + dGCLdOM2               &
-            + dPOLdOM2
+            eps2der * eps2rt_om2   &
+          + 2.0D0 * alf2 * eps3der &
+          + sigder * sigsq_om2     &
+          + dCAVdOM2               &
+          + dGCLdOM2               &
+          + dPOLdOM2
 
        eom12 =    &
 
        eom12 =    &
-              evdwij  * eps1_om12     &
-            + eps2der * eps2rt_om12   &
-            - 2.0D0 * alf12 * eps3der &
-            + sigder *sigsq_om12      &
-            + dCAVdOM12               &
-            + dGCLdOM12
+            evdwij  * eps1_om12     &
+          + eps2der * eps2rt_om12   &
+          - 2.0D0 * alf12 * eps3der &
+          + sigder *sigsq_om12      &
+          + dCAVdOM12               &
+          + dGCLdOM12
 !        om12=0.0
 !        eom12=0.0
 !       print *,eom1,eom2,eom12,om12,i,j,"eom1,2,12",erij(1),erij(2),erij(3)
 !        om12=0.0
 !        eom12=0.0
 !       print *,eom1,eom2,eom12,om12,i,j,"eom1,2,12",erij(1),erij(2),erij(3)
@@ -24675,24 +24647,24 @@
 !       print *,dsci_inv,dscj_inv,dc_norm(2,nres+j),dc_norm(2,nres+i),&
 !               gg(1),gg(2),"rozne"
        DO k = 1, 3
 !       print *,dsci_inv,dscj_inv,dc_norm(2,nres+j),dc_norm(2,nres+i),&
 !               gg(1),gg(2),"rozne"
        DO k = 1, 3
-        dcosom1(k) = rij * (dc_norm(k,i) - om1 * erij(k))
-        dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
-        gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
-        gvdwc_pepbase(k,i)= gvdwc_pepbase(k,i) +0.5*(- gg(k))   &
-                 + (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i)))&
-                 *dsci_inv*2.0 &
-                 - (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
-        gvdwc_pepbase(k,i+1)= gvdwc_pepbase(k,i+1) +0.5*(- gg(k))   &
-                 - (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i))) &
-                 *dsci_inv*2.0 &
-                 + (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
+      dcosom1(k) = rij * (dc_norm(k,i) - om1 * erij(k))
+      dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
+      gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
+      gvdwc_pepbase(k,i)= gvdwc_pepbase(k,i) +0.5*(- gg(k))   &
+             + (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i)))&
+             *dsci_inv*2.0 &
+             - (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
+      gvdwc_pepbase(k,i+1)= gvdwc_pepbase(k,i+1) +0.5*(- gg(k))   &
+             - (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i))) &
+             *dsci_inv*2.0 &
+             + (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
 !         print *,eom12,eom2,om12,om2
 !eom12*(-dc_norm(k,i)/2.0-om12*dc_norm(k,nres+j)),&
 !                (eom2*(erij(k)-om2*dc_norm(k,nres+j)))
 !         print *,eom12,eom2,om12,om2
 !eom12*(-dc_norm(k,i)/2.0-om12*dc_norm(k,nres+j)),&
 !                (eom2*(erij(k)-om2*dc_norm(k,nres+j)))
-        gvdwx_pepbase(k,j)= gvdwx_pepbase(k,j) + gg(k)  &
-                 + (eom12*(dc_norm(k,i)-om12*dc_norm(k,nres+j))&
-                 + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
-        gvdwc_pepbase(k,j)=gvdwc_pepbase(k,j)+gg(k)
+      gvdwx_pepbase(k,j)= gvdwx_pepbase(k,j) + gg(k)  &
+             + (eom12*(dc_norm(k,i)-om12*dc_norm(k,nres+j))&
+             + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+      gvdwc_pepbase(k,j)=gvdwc_pepbase(k,j)+gg(k)
        END DO
        RETURN
       END SUBROUTINE sc_grad_pepbase
        END DO
        RETURN
       END SUBROUTINE sc_grad_pepbase
@@ -24715,124 +24687,92 @@
 !el local variables
       integer :: iint,itypi,itypi1,itypj,subchap
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
 !el local variables
       integer :: iint,itypi,itypi1,itypj,subchap
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
-      real(kind=8) :: evdw,sig0ij
+      real(kind=8) :: evdw,sig0ij,aa,bb
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
-                    dist_temp, dist_init,aa,bb,ssgradlipi,ssgradlipj, &
-                    sslipi,sslipj,faclip,alpha_sco
+                dist_temp, dist_init,ssgradlipi,ssgradlipj, &
+                sslipi,sslipj,faclip,alpha_sco
       integer :: ii
       real(kind=8) :: fracinbuf
        real (kind=8) :: escpho
        real (kind=8),dimension(4):: ener
        real(kind=8) :: b1,b2,b3,b4,egb,eps_in,eps_inout_fac,eps_out
        real(kind=8) :: ECL,Elj,Equad,Epol,eheadtail,rhead,dGCLOM2,&
       integer :: ii
       real(kind=8) :: fracinbuf
        real (kind=8) :: escpho
        real (kind=8),dimension(4):: ener
        real(kind=8) :: b1,b2,b3,b4,egb,eps_in,eps_inout_fac,eps_out
        real(kind=8) :: ECL,Elj,Equad,Epol,eheadtail,rhead,dGCLOM2,&
-        sqom1,sqom2,sqom12,c1,c2,pom,Lambf,sparrow,&
-        Chif,ChiLambf,bat,eagle,top,bot,botsq,Fcav,dtop,dFdR,dFdOM1,&
-        dFdOM2,w1,w2,dGCLdR,dFdL,dFdOM12,dbot ,&
-        r1,eps_head,alphapol1,pis,facd2,d2,facd1,d1,erdxj,erdxi,federmaus,&
-        dPOLdR1,dFGBdOM2,dFGBdR1,dPOLdFGB1,RR1,MomoFac1,hawk,d1i,d1j,&
-        sig1,sig2,chis12,chis2,ee1,fgb1,a12sq,chis1,Rhead_sq,Qij,dFGBdOM1
+      sqom1,sqom2,sqom12,c1,c2,pom,Lambf,sparrow,&
+      Chif,ChiLambf,bat,eagle,top,bot,botsq,Fcav,dtop,dFdR,dFdOM1,&
+      dFdOM2,w1,w2,dGCLdR,dFdL,dFdOM12,dbot ,&
+      r1,eps_head,alphapol1,pis,facd2,d2,facd1,d1,erdxj,erdxi,federmaus,&
+      dPOLdR1,dFGBdOM2,dFGBdR1,dPOLdFGB1,RR1,MomoFac1,hawk,d1i,d1j,&
+      sig1,sig2,chis12,chis2,ee1,fgb1,a12sq,chis1,Rhead_sq,Qij,dFGBdOM1
        real(kind=8),dimension(3,2)::chead,erhead_tail
        real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead
        real(kind=8),dimension(3,2)::chead,erhead_tail
        real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead
-       integer troll
-       eps_out=80.0d0
-       escpho=0.0d0
-!       do i=1,nres_molec(1)
-        do i=ibond_start,ibond_end
-        if (itype(i,1).eq.ntyp1_molec(1)) cycle
-        itypi  = itype(i,1)
-        dxi    = dc_norm(1,nres+i)
-        dyi    = dc_norm(2,nres+i)
-        dzi    = dc_norm(3,nres+i)
-        dsci_inv = vbld_inv(i+nres)
-        xi=c(1,nres+i)
-        yi=c(2,nres+i)
-        zi=c(3,nres+i)
-        xi=mod(xi,boxxsize)
-         if (xi.lt.0) xi=xi+boxxsize
-        yi=mod(yi,boxysize)
-         if (yi.lt.0) yi=yi+boxysize
-        zi=mod(zi,boxzsize)
-         if (zi.lt.0) zi=zi+boxzsize
-         do j=nres_molec(1)+1,nres_molec(2)+nres_molec(1)-1
-           itypj= itype(j,2)
-           if ((itype(j,2).eq.ntyp1_molec(2)).or.&
-            (itype(j+1,2).eq.ntyp1_molec(2))) cycle
-           xj=(c(1,j)+c(1,j+1))/2.0
-           yj=(c(2,j)+c(2,j+1))/2.0
-           zj=(c(3,j)+c(3,j+1))/2.0
-           xj=dmod(xj,boxxsize)
-           if (xj.lt.0) xj=xj+boxxsize
-           yj=dmod(yj,boxysize)
-           if (yj.lt.0) yj=yj+boxysize
-           zj=dmod(zj,boxzsize)
-           if (zj.lt.0) zj=zj+boxzsize
-          dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          xj_safe=xj
-          yj_safe=yj
-          zj_safe=zj
-          subchap=0
-          do xshift=-1,1
-          do yshift=-1,1
-          do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-          enddo
-          enddo
-          enddo
-          if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-          else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-          endif
+       integer troll
+       eps_out=80.0d0
+       escpho=0.0d0
+!       do i=1,nres_molec(1)
+      do i=ibond_start,ibond_end
+      if (itype(i,1).eq.ntyp1_molec(1)) cycle
+      itypi  = itype(i,1)
+      dxi    = dc_norm(1,nres+i)
+      dyi    = dc_norm(2,nres+i)
+      dzi    = dc_norm(3,nres+i)
+      dsci_inv = vbld_inv(i+nres)
+      xi=c(1,nres+i)
+      yi=c(2,nres+i)
+      zi=c(3,nres+i)
+       call to_box(xi,yi,zi)
+      call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+       do j=nres_molec(1)+1,nres_molec(2)+nres_molec(1)-1
+         itypj= itype(j,2)
+         if ((itype(j,2).eq.ntyp1_molec(2)).or.&
+          (itype(j+1,2).eq.ntyp1_molec(2))) cycle
+         xj=(c(1,j)+c(1,j+1))/2.0
+         yj=(c(2,j)+c(2,j+1))/2.0
+         zj=(c(3,j)+c(3,j+1))/2.0
+     call to_box(xj,yj,zj)
+!     call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+!      aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+!       +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+!      bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+!       +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)
           dxj = dc_norm( 1,j )
           dxj = dc_norm( 1,j )
-          dyj = dc_norm( 2,j )
-          dzj = dc_norm( 3,j )
-          dscj_inv = vbld_inv(j+1)
+        dyj = dc_norm( 2,j )
+        dzj = dc_norm( 3,j )
+        dscj_inv = vbld_inv(j+1)
 
 ! Gay-berne var's
 
 ! Gay-berne var's
-          sig0ij = sigma_scpho(itypi )
-          chi1   = chi_scpho(itypi,1 )
-          chi2   = chi_scpho(itypi,2 )
+        sig0ij = sigma_scpho(itypi )
+        chi1   = chi_scpho(itypi,1 )
+        chi2   = chi_scpho(itypi,2 )
 !          chi1=0.0d0
 !          chi2=0.0d0
 !          chi1=0.0d0
 !          chi2=0.0d0
-          chi12  = chi1 * chi2
-          chip1  = chipp_scpho(itypi,1 )
-          chip2  = chipp_scpho(itypi,2 )
+        chi12  = chi1 * chi2
+        chip1  = chipp_scpho(itypi,1 )
+        chip2  = chipp_scpho(itypi,2 )
 !          chip1=0.0d0
 !          chip2=0.0d0
 !          chip1=0.0d0
 !          chip2=0.0d0
-          chip12 = chip1 * chip2
-          chis1 = chis_scpho(itypi,1)
-          chis2 = chis_scpho(itypi,2)
-          chis12 = chis1 * chis2
-          sig1 = sigmap1_scpho(itypi)
-          sig2 = sigmap2_scpho(itypi)
+        chip12 = chip1 * chip2
+        chis1 = chis_scpho(itypi,1)
+        chis2 = chis_scpho(itypi,2)
+        chis12 = chis1 * chis2
+        sig1 = sigmap1_scpho(itypi)
+        sig2 = sigmap2_scpho(itypi)
 !       write (*,*) "sig1 = ", sig1
 !       write (*,*) "sig1 = ", sig1
 !       write (*,*) "sig2 = ", sig2
 ! alpha factors from Fcav/Gcav
 !       write (*,*) "sig1 = ", sig1
 !       write (*,*) "sig1 = ", sig1
 !       write (*,*) "sig2 = ", sig2
 ! alpha factors from Fcav/Gcav
-          alf1   = 0.0d0
-          alf2   = 0.0d0
-          alf12  = 0.0d0
-          a12sq = rborn_scphoi(itypi) * rborn_scphoj(itypi)
+        alf1   = 0.0d0
+        alf2   = 0.0d0
+        alf12  = 0.0d0
+        a12sq = rborn_scphoi(itypi) * rborn_scphoj(itypi)
 
 
-          b1 = alphasur_scpho(1,itypi)
+        b1 = alphasur_scpho(1,itypi)
 !          b1=0.0d0
 !          b1=0.0d0
-          b2 = alphasur_scpho(2,itypi)
-          b3 = alphasur_scpho(3,itypi)
-          b4 = alphasur_scpho(4,itypi)
+        b2 = alphasur_scpho(2,itypi)
+        b3 = alphasur_scpho(3,itypi)
+        b4 = alphasur_scpho(4,itypi)
 ! used to determine whether we want to do quadrupole calculations
 ! used by Fgb
        eps_in = epsintab_scpho(itypi)
 ! used to determine whether we want to do quadrupole calculations
 ! used by Fgb
        eps_in = epsintab_scpho(itypi)
@@ -24841,24 +24781,24 @@
 !       write (*,*) "eps_inout_fac = ", eps_inout_fac
 !-------------------------------------------------------------------
 ! tail location and distance calculations
 !       write (*,*) "eps_inout_fac = ", eps_inout_fac
 !-------------------------------------------------------------------
 ! tail location and distance calculations
-          d1i = dhead_scphoi(itypi) !this is shift of dipole/charge
-          d1j = 0.0
+        d1i = dhead_scphoi(itypi) !this is shift of dipole/charge
+        d1j = 0.0
        DO k = 1,3
 ! location of polar head is computed by taking hydrophobic centre
 ! and moving by a d1 * dc_norm vector
 ! see unres publications for very informative images
        DO k = 1,3
 ! location of polar head is computed by taking hydrophobic centre
 ! and moving by a d1 * dc_norm vector
 ! see unres publications for very informative images
-        chead(k,1) = c(k, i+nres) + d1i * dc_norm(k, i+nres)
-        chead(k,2) = (c(k, j) + c(k, j+1))/2.0
+      chead(k,1) = c(k, i+nres) + d1i * dc_norm(k, i+nres)
+      chead(k,2) = (c(k, j) + c(k, j+1))/2.0
 ! distance 
 !        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
 !        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
 ! distance 
 !        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
 !        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
-        Rhead_distance(k) = chead(k,2) - chead(k,1)
+      Rhead_distance(k) = chead(k,2) - chead(k,1)
        END DO
 ! pitagoras (root of sum of squares)
        Rhead = dsqrt( &
        END DO
 ! pitagoras (root of sum of squares)
        Rhead = dsqrt( &
-          (Rhead_distance(1)*Rhead_distance(1)) &
-        + (Rhead_distance(2)*Rhead_distance(2)) &
-        + (Rhead_distance(3)*Rhead_distance(3)))
+        (Rhead_distance(1)*Rhead_distance(1)) &
+      + (Rhead_distance(2)*Rhead_distance(2)) &
+      + (Rhead_distance(3)*Rhead_distance(3)))
        Rhead_sq=Rhead**2.0
 !-------------------------------------------------------------------
 ! zero everything that should be zero'ed
        Rhead_sq=Rhead**2.0
 !-------------------------------------------------------------------
 ! zero everything that should be zero'ed
@@ -24875,104 +24815,104 @@
        dGCLdOM12 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0
        dGCLdOM12 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0
-          Fcav = 0.0d0
-          dFdR = 0.0d0
-          dCAVdOM1  = 0.0d0
-          dCAVdOM2  = 0.0d0
-          dCAVdOM12 = 0.0d0
-          dscj_inv = vbld_inv(j+1)/2.0
+        Fcav = 0.0d0
+        dFdR = 0.0d0
+        dCAVdOM1  = 0.0d0
+        dCAVdOM2  = 0.0d0
+        dCAVdOM12 = 0.0d0
+        dscj_inv = vbld_inv(j+1)/2.0
 !dhead_scbasej(itypi,itypj)
 !          print *,i,j,dscj_inv,dsci_inv
 ! rij holds 1/(distance of Calpha atoms)
 !dhead_scbasej(itypi,itypj)
 !          print *,i,j,dscj_inv,dsci_inv
 ! rij holds 1/(distance of Calpha atoms)
-          rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
-          rij  = dsqrt(rrij)
+        rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
+        rij  = dsqrt(rrij)
 !----------------------------
 !----------------------------
-          CALL sc_angular
+        CALL sc_angular
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials
 ! om = omega, sqom = om^2
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials
 ! om = omega, sqom = om^2
-          sqom1  = om1 * om1
-          sqom2  = om2 * om2
-          sqom12 = om12 * om12
+        sqom1  = om1 * om1
+        sqom2  = om2 * om2
+        sqom12 = om12 * om12
 
 ! now we calculate EGB - Gey-Berne
 ! It will be summed up in evdwij and saved in evdw
 
 ! now we calculate EGB - Gey-Berne
 ! It will be summed up in evdwij and saved in evdw
-          sigsq     = 1.0D0  / sigsq
-          sig       = sig0ij * dsqrt(sigsq)
+        sigsq     = 1.0D0  / sigsq
+        sig       = sig0ij * dsqrt(sigsq)
 !          rij_shift = 1.0D0  / rij - sig + sig0ij
 !          rij_shift = 1.0D0  / rij - sig + sig0ij
-          rij_shift = 1.0/rij - sig + sig0ij
-          IF (rij_shift.le.0.0D0) THEN
-           evdw = 1.0D20
-           RETURN
-          END IF
-          sigder = -sig * sigsq
-          rij_shift = 1.0D0 / rij_shift
-          fac       = rij_shift**expon
-          c1        = fac  * fac * aa_scpho(itypi)
+        rij_shift = 1.0/rij - sig + sig0ij
+        IF (rij_shift.le.0.0D0) THEN
+         evdw = 1.0D20
+         RETURN
+        END IF
+        sigder = -sig * sigsq
+        rij_shift = 1.0D0 / rij_shift
+        fac       = rij_shift**expon
+        c1        = fac  * fac * aa_scpho(itypi)
 !          c1        = 0.0d0
 !          c1        = 0.0d0
-          c2        = fac  * bb_scpho(itypi)
+        c2        = fac  * bb_scpho(itypi)
 !          c2        = 0.0d0
 !          c2        = 0.0d0
-          evdwij    = eps1 * eps2rt * eps3rt * ( c1 + c2 )
-          eps2der   = eps3rt * evdwij
-          eps3der   = eps2rt * evdwij
+        evdwij    = eps1 * eps2rt * eps3rt * ( c1 + c2 )
+        eps2der   = eps3rt * evdwij
+        eps3der   = eps2rt * evdwij
 !          evdwij    = 4.0d0 * eps2rt * eps3rt * evdwij
 !          evdwij    = 4.0d0 * eps2rt * eps3rt * evdwij
-          evdwij    = eps2rt * eps3rt * evdwij
-          c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
-          fac    = -expon * (c1 + evdwij) * rij_shift
-          sigder = fac * sigder
+        evdwij    = eps2rt * eps3rt * evdwij
+        c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
+        fac    = -expon * (c1 + evdwij) * rij_shift
+        sigder = fac * sigder
 !          fac    = rij * fac
 ! Calculate distance derivative
 !          fac    = rij * fac
 ! Calculate distance derivative
-          gg(1) =  fac
-          gg(2) =  fac
-          gg(3) =  fac
-          fac = chis1 * sqom1 + chis2 * sqom2 &
-          - 2.0d0 * chis12 * om1 * om2 * om12
+        gg(1) =  fac
+        gg(2) =  fac
+        gg(3) =  fac
+        fac = chis1 * sqom1 + chis2 * sqom2 &
+        - 2.0d0 * chis12 * om1 * om2 * om12
 ! we will use pom later in Gcav, so dont mess with it!
 ! we will use pom later in Gcav, so dont mess with it!
-          pom = 1.0d0 - chis1 * chis2 * sqom12
-          Lambf = (1.0d0 - (fac / pom))
-          Lambf = dsqrt(Lambf)
-          sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
+        pom = 1.0d0 - chis1 * chis2 * sqom12
+        Lambf = (1.0d0 - (fac / pom))
+        Lambf = dsqrt(Lambf)
+        sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
 !       write (*,*) "sparrow = ", sparrow
 !       write (*,*) "sparrow = ", sparrow
-          Chif = 1.0d0/rij * sparrow
-          ChiLambf = Chif * Lambf
-          eagle = dsqrt(ChiLambf)
-          bat = ChiLambf ** 11.0d0
-          top = b1 * ( eagle + b2 * ChiLambf - b3 )
-          bot = 1.0d0 + b4 * (ChiLambf ** 12.0d0)
-          botsq = bot * bot
-          Fcav = top / bot
-          dtop = b1 * ((Lambf / (2.0d0 * eagle)) + (b2 * Lambf))
-          dbot = 12.0d0 * b4 * bat * Lambf
-          dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
+        Chif = 1.0d0/rij * sparrow
+        ChiLambf = Chif * Lambf
+        eagle = dsqrt(ChiLambf)
+        bat = ChiLambf ** 11.0d0
+        top = b1 * ( eagle + b2 * ChiLambf - b3 )
+        bot = 1.0d0 + b4 * (ChiLambf ** 12.0d0)
+        botsq = bot * bot
+        Fcav = top / bot
+        dtop = b1 * ((Lambf / (2.0d0 * eagle)) + (b2 * Lambf))
+        dbot = 12.0d0 * b4 * bat * Lambf
+        dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
 !       dFdR = 0.0d0
 !      write (*,*) "dFcav/dR = ", dFdR
 !       dFdR = 0.0d0
 !      write (*,*) "dFcav/dR = ", dFdR
-          dtop = b1 * ((Chif / (2.0d0 * eagle)) + (b2 * Chif))
-          dbot = 12.0d0 * b4 * bat * Chif
-          eagle = Lambf * pom
-          dFdOM1  = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
-          dFdOM2  = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
-          dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
-              * (chis2 * om2 * om12 - om1) / (eagle * pom)
-
-          dFdL = ((dtop * bot - top * dbot) / botsq)
+        dtop = b1 * ((Chif / (2.0d0 * eagle)) + (b2 * Chif))
+        dbot = 12.0d0 * b4 * bat * Chif
+        eagle = Lambf * pom
+        dFdOM1  = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
+        dFdOM2  = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
+        dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
+            * (chis2 * om2 * om12 - om1) / (eagle * pom)
+
+        dFdL = ((dtop * bot - top * dbot) / botsq)
 !       dFdL = 0.0d0
 !       dFdL = 0.0d0
-          dCAVdOM1  = dFdL * ( dFdOM1 )
-          dCAVdOM2  = dFdL * ( dFdOM2 )
-          dCAVdOM12 = dFdL * ( dFdOM12 )
+        dCAVdOM1  = dFdL * ( dFdOM1 )
+        dCAVdOM2  = dFdL * ( dFdOM2 )
+        dCAVdOM12 = dFdL * ( dFdOM12 )
 
 
-          ertail(1) = xj*rij
-          ertail(2) = yj*rij
-          ertail(3) = zj*rij
+        ertail(1) = xj*rij
+        ertail(2) = yj*rij
+        ertail(3) = zj*rij
        DO k = 1, 3
 !      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
 !         if (i.eq.3) print *,'decl0',gvdwx_scpho(k,i),i
 
        DO k = 1, 3
 !      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
 !         if (i.eq.3) print *,'decl0',gvdwx_scpho(k,i),i
 
-        pom = ertail(k)
+      pom = ertail(k)
 !        print *,pom,gg(k),dFdR
 !-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
 !        print *,pom,gg(k),dFdR
 !-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
-        gvdwx_scpho(k,i) = gvdwx_scpho(k,i) &
-                  - (( dFdR + gg(k) ) * pom)
+      gvdwx_scpho(k,i) = gvdwx_scpho(k,i) &
+              - (( dFdR + gg(k) ) * pom)
 !                 +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
 !                 +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
 !     &             - ( dFdR * pom )
 !                 +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
 !                 +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
 !     &             - ( dFdR * pom )
@@ -24984,20 +24924,20 @@
 !                 +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
 !c!     &             + ( dFdR * pom )
 
 !                 +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
 !c!     &             + ( dFdR * pom )
 
-        gvdwc_scpho(k,i) = gvdwc_scpho(k,i) &
-                  - (( dFdR + gg(k) ) * ertail(k))
+      gvdwc_scpho(k,i) = gvdwc_scpho(k,i) &
+              - (( dFdR + gg(k) ) * ertail(k))
 !c!     &             - ( dFdR * ertail(k))
 
 !c!     &             - ( dFdR * ertail(k))
 
-        gvdwc_scpho(k,j) = gvdwc_scpho(k,j) &
-                  + (( dFdR + gg(k) ) * ertail(k))/2.0
+      gvdwc_scpho(k,j) = gvdwc_scpho(k,j) &
+              + (( dFdR + gg(k) ) * ertail(k))/2.0
 
 
-        gvdwc_scpho(k,j+1) = gvdwc_scpho(k,j+1) &
-                  + (( dFdR + gg(k) ) * ertail(k))/2.0
+      gvdwc_scpho(k,j+1) = gvdwc_scpho(k,j+1) &
+              + (( dFdR + gg(k) ) * ertail(k))/2.0
 
 !c!     &             + ( dFdR * ertail(k))
 
 
 !c!     &             + ( dFdR * ertail(k))
 
-        gg(k) = 0.0d0
-        ENDDO
+      gg(k) = 0.0d0
+      ENDDO
 !c!      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !c!      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
 !      alphapol1 = alphapol_scpho(itypi)
 !c!      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !c!      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
 !      alphapol1 = alphapol_scpho(itypi)
@@ -25008,7 +24948,7 @@
        Ecl = (332.0d0 * Qij*dexp(-Rhead*alpha_sco)) / Rhead
 !c! derivative of Ecl is Gcl...
        dGCLdR = (-332.0d0 * Qij*dexp(-Rhead*alpha_sco)*  &
        Ecl = (332.0d0 * Qij*dexp(-Rhead*alpha_sco)) / Rhead
 !c! derivative of Ecl is Gcl...
        dGCLdR = (-332.0d0 * Qij*dexp(-Rhead*alpha_sco)*  &
-                (Rhead*alpha_sco+1) ) / Rhead_sq
+            (Rhead*alpha_sco+1) ) / Rhead_sq
        if (energy_dec) write(iout,*) "ECL",ECL,Rhead,1.0/rij
        else if (wqdip_scpho(2,itypi).gt.0.0d0) then
        w1        = wqdip_scpho(1,itypi)
        if (energy_dec) write(iout,*) "ECL",ECL,Rhead,1.0/rij
        else if (wqdip_scpho(2,itypi).gt.0.0d0) then
        w1        = wqdip_scpho(1,itypi)
@@ -25029,15 +24969,15 @@
        sparrow  = w1  *  om1
        hawk     = w2 *  (1.0d0 - sqom2)
        Ecl = sparrow / Rhead**2.0d0 &
        sparrow  = w1  *  om1
        hawk     = w2 *  (1.0d0 - sqom2)
        Ecl = sparrow / Rhead**2.0d0 &
-           - hawk    / Rhead**4.0d0
+         - hawk    / Rhead**4.0d0
 !c!-------------------------------------------------------------------
        if (energy_dec) write(iout,*) "ECLdipdip",ECL,Rhead,&
 !c!-------------------------------------------------------------------
        if (energy_dec) write(iout,*) "ECLdipdip",ECL,Rhead,&
-           1.0/rij,sparrow
+         1.0/rij,sparrow
 
 !c! derivative of ecl is Gcl
 !c! dF/dr part
        dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
 
 !c! derivative of ecl is Gcl
 !c! dF/dr part
        dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
-                + 4.0d0 * hawk    / Rhead**5.0d0
+            + 4.0d0 * hawk    / Rhead**5.0d0
 !c! dF/dom1
        dGCLdOM1 = (w1) / (Rhead**2.0d0)
 !c! dF/dom2
 !c! dF/dom1
        dGCLdOM1 = (w1) / (Rhead**2.0d0)
 !c! dF/dom2
@@ -25050,7 +24990,7 @@
        R1 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances tail is center of side-chain
        R1 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances tail is center of side-chain
-        R1=R1+((c(k,j)+c(k,j+1))/2.0-chead(k,1))**2
+      R1=R1+((c(k,j)+c(k,j+1))/2.0-chead(k,1))**2
        END DO
 !c! Pitagoras
        R1 = dsqrt(R1)
        END DO
 !c! Pitagoras
        R1 = dsqrt(R1)
@@ -25066,25 +25006,25 @@
        epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0)
 ! derivative of Epol is Gpol...
        dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0) &
        epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0)
 ! derivative of Epol is Gpol...
        dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0) &
-                / (fgb1 ** 5.0d0)
+            / (fgb1 ** 5.0d0)
        dFGBdR1 = ( (R1 / MomoFac1) &
        dFGBdR1 = ( (R1 / MomoFac1) &
-             * ( 2.0d0 - (0.5d0 * ee1) ) ) &
-             / ( 2.0d0 * fgb1 )
+           * ( 2.0d0 - (0.5d0 * ee1) ) ) &
+           / ( 2.0d0 * fgb1 )
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
-               * (2.0d0 - 0.5d0 * ee1) ) &
-               / (2.0d0 * fgb1)
+             * (2.0d0 - 0.5d0 * ee1) ) &
+             / (2.0d0 * fgb1)
        dPOLdR1 = dPOLdFGB1 * dFGBdR1
 !       dPOLdR1 = 0.0d0
 !       dPOLdOM1 = 0.0d0
        dFGBdOM1 = (((R1 * R1 * chi2 * om1) / (MomoFac1 * MomoFac1)) &
        dPOLdR1 = dPOLdFGB1 * dFGBdR1
 !       dPOLdR1 = 0.0d0
 !       dPOLdOM1 = 0.0d0
        dFGBdOM1 = (((R1 * R1 * chi2 * om1) / (MomoFac1 * MomoFac1)) &
-               * (2.0d0 - 0.5d0 * ee1) ) &
-               / (2.0d0 * fgb1)
+             * (2.0d0 - 0.5d0 * ee1) ) &
+             / (2.0d0 * fgb1)
 
        dPOLdOM1 = dPOLdFGB1 * dFGBdOM1
        dPOLdOM2 = 0.0
        DO k = 1, 3
 
        dPOLdOM1 = dPOLdFGB1 * dFGBdOM1
        dPOLdOM2 = 0.0
        DO k = 1, 3
-        erhead(k) = Rhead_distance(k)/Rhead
-        erhead_tail(k,1) = (((c(k,j)+c(k,j+1))/2.0-chead(k,1))/R1)
+      erhead(k) = Rhead_distance(k)/Rhead
+      erhead_tail(k,1) = (((c(k,j)+c(k,j+1))/2.0-chead(k,1))/R1)
        END DO
 
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
        END DO
 
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
@@ -25097,38 +25037,38 @@
 !       facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
 
        DO k = 1, 3
 !       facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
 
        DO k = 1, 3
-        hawk = (erhead_tail(k,1) + &
-        facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
+      hawk = (erhead_tail(k,1) + &
+      facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
 !        facd1=0.0d0
 !        facd2=0.0d0
 !         if (i.eq.3) print *,'decl1',dGCLdR,dPOLdR1,gvdwc_scpho(k,i),i,&
 !                pom,(erhead_tail(k,1))
 
 !        print *,'decl',dGCLdR,dPOLdR1,gvdwc_scpho(k,i)
 !        facd1=0.0d0
 !        facd2=0.0d0
 !         if (i.eq.3) print *,'decl1',dGCLdR,dPOLdR1,gvdwc_scpho(k,i),i,&
 !                pom,(erhead_tail(k,1))
 
 !        print *,'decl',dGCLdR,dPOLdR1,gvdwc_scpho(k,i)
-        pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
-        gvdwx_scpho(k,i) = gvdwx_scpho(k,i)   &
-                   - dGCLdR * pom &
-                   - dPOLdR1 *  (erhead_tail(k,1))
+      pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+      gvdwx_scpho(k,i) = gvdwx_scpho(k,i)   &
+               - dGCLdR * pom &
+               - dPOLdR1 *  (erhead_tail(k,1))
 !     &             - dGLJdR * pom
 
 !     &             - dGLJdR * pom
 
-        pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j))
+      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j))
 !        gvdwx_scpho(k,j) = gvdwx_scpho(k,j)    &
 !                   + dGCLdR * pom  &
 !                   + dPOLdR1 * (erhead_tail(k,1))
 !     &             + dGLJdR * pom
 
 
 !        gvdwx_scpho(k,j) = gvdwx_scpho(k,j)    &
 !                   + dGCLdR * pom  &
 !                   + dPOLdR1 * (erhead_tail(k,1))
 !     &             + dGLJdR * pom
 
 
-        gvdwc_scpho(k,i) = gvdwc_scpho(k,i)  &
-                  - dGCLdR * erhead(k) &
-                  - dPOLdR1 * erhead_tail(k,1)
+      gvdwc_scpho(k,i) = gvdwc_scpho(k,i)  &
+              - dGCLdR * erhead(k) &
+              - dPOLdR1 * erhead_tail(k,1)
 !     &             - dGLJdR * erhead(k)
 
 !     &             - dGLJdR * erhead(k)
 
-        gvdwc_scpho(k,j) = gvdwc_scpho(k,j)         &
-                  + (dGCLdR * erhead(k)  &
-                  + dPOLdR1 * erhead_tail(k,1))/2.0
-        gvdwc_scpho(k,j+1) = gvdwc_scpho(k,j+1)         &
-                  + (dGCLdR * erhead(k)  &
-                  + dPOLdR1 * erhead_tail(k,1))/2.0
+      gvdwc_scpho(k,j) = gvdwc_scpho(k,j)         &
+              + (dGCLdR * erhead(k)  &
+              + dPOLdR1 * erhead_tail(k,1))/2.0
+      gvdwc_scpho(k,j+1) = gvdwc_scpho(k,j+1)         &
+              + (dGCLdR * erhead(k)  &
+              + dPOLdR1 * erhead_tail(k,1))/2.0
 
 !     &             + dGLJdR * erhead(k)
 !        if (i.eq.3) print *,'decl2',dGCLdR,dPOLdR1,gvdwc_scpho(k,i),i
 
 !     &             + dGLJdR * erhead(k)
 !        if (i.eq.3) print *,'decl2',dGCLdR,dPOLdR1,gvdwc_scpho(k,i),i
@@ -25136,10 +25076,10 @@
        END DO
 !       if (i.eq.3) print *,i,j,evdwij,epol,Fcav,ECL
        if (energy_dec) write (iout,'(a22,2i5,4f8.3,f16.3)'), &
        END DO
 !       if (i.eq.3) print *,i,j,evdwij,epol,Fcav,ECL
        if (energy_dec) write (iout,'(a22,2i5,4f8.3,f16.3)'), &
-        "escpho:evdw,pol,cav,CL",i,j,evdwij,epol,Fcav,ECL,escpho
+      "escpho:evdw,pol,cav,CL",i,j,evdwij,epol,Fcav,ECL,escpho
        escpho=escpho+evdwij+epol+Fcav+ECL
        call sc_grad_scpho
        escpho=escpho+evdwij+epol+Fcav+ECL
        call sc_grad_scpho
-         enddo
+       enddo
 
       enddo
 
 
       enddo
 
@@ -25150,28 +25090,28 @@
 
        real (kind=8) :: dcosom1(3),dcosom2(3)
        eom1  =    &
 
        real (kind=8) :: dcosom1(3),dcosom2(3)
        eom1  =    &
-              eps2der * eps2rt_om1   &
-            - 2.0D0 * alf1 * eps3der &
-            + sigder * sigsq_om1     &
-            + dCAVdOM1               &
-            + dGCLdOM1               &
-            + dPOLdOM1
+            eps2der * eps2rt_om1   &
+          - 2.0D0 * alf1 * eps3der &
+          + sigder * sigsq_om1     &
+          + dCAVdOM1               &
+          + dGCLdOM1               &
+          + dPOLdOM1
 
        eom2  =  &
 
        eom2  =  &
-              eps2der * eps2rt_om2   &
-            + 2.0D0 * alf2 * eps3der &
-            + sigder * sigsq_om2     &
-            + dCAVdOM2               &
-            + dGCLdOM2               &
-            + dPOLdOM2
+            eps2der * eps2rt_om2   &
+          + 2.0D0 * alf2 * eps3der &
+          + sigder * sigsq_om2     &
+          + dCAVdOM2               &
+          + dGCLdOM2               &
+          + dPOLdOM2
 
        eom12 =    &
 
        eom12 =    &
-              evdwij  * eps1_om12     &
-            + eps2der * eps2rt_om12   &
-            - 2.0D0 * alf12 * eps3der &
-            + sigder *sigsq_om12      &
-            + dCAVdOM12               &
-            + dGCLdOM12
+            evdwij  * eps1_om12     &
+          + eps2der * eps2rt_om12   &
+          - 2.0D0 * alf12 * eps3der &
+          + sigder *sigsq_om12      &
+          + dCAVdOM12               &
+          + dGCLdOM12
 !        om12=0.0
 !        eom12=0.0
 !       print *,eom1,eom2,eom12,om12,i,j,"eom1,2,12",erij(1),erij(2),erij(3)
 !        om12=0.0
 !        eom12=0.0
 !       print *,eom1,eom2,eom12,om12,i,j,"eom1,2,12",erij(1),erij(2),erij(3)
@@ -25181,20 +25121,20 @@
 !       print *,dsci_inv,dscj_inv,dc_norm(2,nres+j),dc_norm(2,nres+i),&
 !               gg(1),gg(2),"rozne"
        DO k = 1, 3
 !       print *,dsci_inv,dscj_inv,dc_norm(2,nres+j),dc_norm(2,nres+i),&
 !               gg(1),gg(2),"rozne"
        DO k = 1, 3
-        dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k))
-        dcosom2(k) = rij * (dc_norm(k,j) - om2 * erij(k))
-        gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
-        gvdwc_scpho(k,j)= gvdwc_scpho(k,j) +0.5*( gg(k))   &
-                 + (-eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,j)))&
-                 *dscj_inv*2.0 &
-                 - (eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv*2.0
-        gvdwc_scpho(k,j+1)= gvdwc_scpho(k,j+1) +0.5*( gg(k))   &
-                 - (-eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,j))) &
-                 *dscj_inv*2.0 &
-                 + (eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv*2.0
-        gvdwx_scpho(k,i)= gvdwx_scpho(k,i) - gg(k)   &
-                 + (eom12*(dc_norm(k,j)-om12*dc_norm(k,nres+i)) &
-                 + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+      dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k))
+      dcosom2(k) = rij * (dc_norm(k,j) - om2 * erij(k))
+      gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
+      gvdwc_scpho(k,j)= gvdwc_scpho(k,j) +0.5*( gg(k))   &
+             + (-eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,j)))&
+             *dscj_inv*2.0 &
+             - (eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv*2.0
+      gvdwc_scpho(k,j+1)= gvdwc_scpho(k,j+1) +0.5*( gg(k))   &
+             - (-eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,j))) &
+             *dscj_inv*2.0 &
+             + (eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv*2.0
+      gvdwx_scpho(k,i)= gvdwx_scpho(k,i) - gg(k)   &
+             + (eom12*(dc_norm(k,j)-om12*dc_norm(k,nres+i)) &
+             + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
 
 !         print *,eom12,eom2,om12,om2
 !eom12*(-dc_norm(k,i)/2.0-om12*dc_norm(k,nres+j)),&
 
 !         print *,eom12,eom2,om12,om2
 !eom12*(-dc_norm(k,i)/2.0-om12*dc_norm(k,nres+j)),&
@@ -25202,7 +25142,7 @@
 !        gvdwx_scpho(k,j)= gvdwx_scpho(k,j) + gg(k)  &
 !                 + (eom12*(dc_norm(k,i)-om12*dc_norm(k,nres+j))&
 !                 + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
 !        gvdwx_scpho(k,j)= gvdwx_scpho(k,j) + gg(k)  &
 !                 + (eom12*(dc_norm(k,i)-om12*dc_norm(k,nres+j))&
 !                 + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
-        gvdwc_scpho(k,i)=gvdwc_scpho(k,i)-gg(k)
+      gvdwc_scpho(k,i)=gvdwc_scpho(k,i)-gg(k)
        END DO
        RETURN
       END SUBROUTINE sc_grad_scpho
        END DO
        RETURN
       END SUBROUTINE sc_grad_scpho
@@ -25227,118 +25167,83 @@
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
       real(kind=8) :: evdw,sig0ij
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
       real(kind=8) :: evdw,sig0ij
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
-                    dist_temp, dist_init,aa,bb,ssgradlipi,ssgradlipj, &
-                    sslipi,sslipj,faclip
+                dist_temp, dist_init,aa,bb,ssgradlipi,ssgradlipj, &
+                sslipi,sslipj,faclip
       integer :: ii
       real(kind=8) :: fracinbuf
        real (kind=8) :: epeppho
        real (kind=8),dimension(4):: ener
        real(kind=8) :: b1,b2,b3,b4,egb,eps_in,eps_inout_fac,eps_out
        real(kind=8) :: ECL,Elj,Equad,Epol,eheadtail,rhead,dGCLOM2,&
       integer :: ii
       real(kind=8) :: fracinbuf
        real (kind=8) :: epeppho
        real (kind=8),dimension(4):: ener
        real(kind=8) :: b1,b2,b3,b4,egb,eps_in,eps_inout_fac,eps_out
        real(kind=8) :: ECL,Elj,Equad,Epol,eheadtail,rhead,dGCLOM2,&
-        sqom1,sqom2,sqom12,c1,c2,pom,Lambf,sparrow,&
-        Chif,ChiLambf,bat,eagle,top,bot,botsq,Fcav,dtop,dFdR,dFdOM1,&
-        dFdOM2,w1,w2,dGCLdR,dFdL,dFdOM12,dbot ,&
-        r1,eps_head,alphapol1,pis,facd2,d2,facd1,d1,erdxj,erdxi,federmaus,&
-        dPOLdR1,dFGBdOM2,dFGBdR1,dPOLdFGB1,RR1,MomoFac1,hawk,d1i,d1j,&
-        sig1,sig2,chis12,chis2,ee1,fgb1,a12sq,chis1,Rhead_sq,Qij,dFGBdOM1
+      sqom1,sqom2,sqom12,c1,c2,pom,Lambf,sparrow,&
+      Chif,ChiLambf,bat,eagle,top,bot,botsq,Fcav,dtop,dFdR,dFdOM1,&
+      dFdOM2,w1,w2,dGCLdR,dFdL,dFdOM12,dbot ,&
+      r1,eps_head,alphapol1,pis,facd2,d2,facd1,d1,erdxj,erdxi,federmaus,&
+      dPOLdR1,dFGBdOM2,dFGBdR1,dPOLdFGB1,RR1,MomoFac1,hawk,d1i,d1j,&
+      sig1,sig2,chis12,chis2,ee1,fgb1,a12sq,chis1,Rhead_sq,Qij,dFGBdOM1
        real(kind=8),dimension(3,2)::chead,erhead_tail
        real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead
        integer troll
        real (kind=8) :: dcosom1(3),dcosom2(3)
        epeppho=0.0d0
 !       do i=1,nres_molec(1)
        real(kind=8),dimension(3,2)::chead,erhead_tail
        real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead
        integer troll
        real (kind=8) :: dcosom1(3),dcosom2(3)
        epeppho=0.0d0
 !       do i=1,nres_molec(1)
-        do i=ibond_start,ibond_end
-        if (itype(i,1).eq.ntyp1_molec(1)) cycle
-        itypi  = itype(i,1)
-        dsci_inv = vbld_inv(i+1)/2.0
-        dxi    = dc_norm(1,i)
-        dyi    = dc_norm(2,i)
-        dzi    = dc_norm(3,i)
-        xi=(c(1,i)+c(1,i+1))/2.0
-        yi=(c(2,i)+c(2,i+1))/2.0
-        zi=(c(3,i)+c(3,i+1))/2.0
-        xi=mod(xi,boxxsize)
-         if (xi.lt.0) xi=xi+boxxsize
-        yi=mod(yi,boxysize)
-         if (yi.lt.0) yi=yi+boxysize
-        zi=mod(zi,boxzsize)
-         if (zi.lt.0) zi=zi+boxzsize
-         do j=nres_molec(1)+1,nres_molec(2)+nres_molec(1)-1
-           itypj= itype(j,2)
-           if ((itype(j,2).eq.ntyp1_molec(2)).or.&
-            (itype(j+1,2).eq.ntyp1_molec(2))) cycle
-           xj=(c(1,j)+c(1,j+1))/2.0
-           yj=(c(2,j)+c(2,j+1))/2.0
-           zj=(c(3,j)+c(3,j+1))/2.0
-           xj=dmod(xj,boxxsize)
-           if (xj.lt.0) xj=xj+boxxsize
-           yj=dmod(yj,boxysize)
-           if (yj.lt.0) yj=yj+boxysize
-           zj=dmod(zj,boxzsize)
-           if (zj.lt.0) zj=zj+boxzsize
-          dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          xj_safe=xj
-          yj_safe=yj
-          zj_safe=zj
-          subchap=0
-          do xshift=-1,1
-          do yshift=-1,1
-          do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-          enddo
-          enddo
-          enddo
-          if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-          else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-          endif
-          rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
-          rij  = dsqrt(rrij)
-          dxj = dc_norm( 1,j )
-          dyj = dc_norm( 2,j )
-          dzj = dc_norm( 3,j )
-          dscj_inv = vbld_inv(j+1)/2.0
+      do i=ibond_start,ibond_end
+      if (itype(i,1).eq.ntyp1_molec(1)) cycle
+      itypi  = itype(i,1)
+      dsci_inv = vbld_inv(i+1)/2.0
+      dxi    = dc_norm(1,i)
+      dyi    = dc_norm(2,i)
+      dzi    = dc_norm(3,i)
+      xi=(c(1,i)+c(1,i+1))/2.0
+      yi=(c(2,i)+c(2,i+1))/2.0
+      zi=(c(3,i)+c(3,i+1))/2.0
+               call to_box(xi,yi,zi)
+
+        do j=nres_molec(1)+1,nres_molec(2)+nres_molec(1)-1
+         itypj= itype(j,2)
+         if ((itype(j,2).eq.ntyp1_molec(2)).or.&
+          (itype(j+1,2).eq.ntyp1_molec(2))) cycle
+         xj=(c(1,j)+c(1,j+1))/2.0
+         yj=(c(2,j)+c(2,j+1))/2.0
+         zj=(c(3,j)+c(3,j+1))/2.0
+                call to_box(xj,yj,zj)
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)
+
+        dist_init=xj**2+yj**2+zj**2
+        rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
+        rij  = dsqrt(rrij)
+        dxj = dc_norm( 1,j )
+        dyj = dc_norm( 2,j )
+        dzj = dc_norm( 3,j )
+        dscj_inv = vbld_inv(j+1)/2.0
 ! Gay-berne var's
 ! Gay-berne var's
-          sig0ij = sigma_peppho
+        sig0ij = sigma_peppho
 !          chi1=0.0d0
 !          chi2=0.0d0
 !          chi1=0.0d0
 !          chi2=0.0d0
-          chi12  = chi1 * chi2
+        chi12  = chi1 * chi2
 !          chip1=0.0d0
 !          chip2=0.0d0
 !          chip1=0.0d0
 !          chip2=0.0d0
-          chip12 = chip1 * chip2
+        chip12 = chip1 * chip2
 !          chis1 = 0.0d0
 !          chis2 = 0.0d0
 !          chis1 = 0.0d0
 !          chis2 = 0.0d0
-          chis12 = chis1 * chis2
-          sig1 = sigmap1_peppho
-          sig2 = sigmap2_peppho
+        chis12 = chis1 * chis2
+        sig1 = sigmap1_peppho
+        sig2 = sigmap2_peppho
 !       write (*,*) "sig1 = ", sig1
 !       write (*,*) "sig1 = ", sig1
 !       write (*,*) "sig2 = ", sig2
 ! alpha factors from Fcav/Gcav
 !       write (*,*) "sig1 = ", sig1
 !       write (*,*) "sig1 = ", sig1
 !       write (*,*) "sig2 = ", sig2
 ! alpha factors from Fcav/Gcav
-          alf1   = 0.0d0
-          alf2   = 0.0d0
-          alf12  = 0.0d0
-          b1 = alphasur_peppho(1)
+        alf1   = 0.0d0
+        alf2   = 0.0d0
+        alf12  = 0.0d0
+        b1 = alphasur_peppho(1)
 !          b1=0.0d0
 !          b1=0.0d0
-          b2 = alphasur_peppho(2)
-          b3 = alphasur_peppho(3)
-          b4 = alphasur_peppho(4)
-          CALL sc_angular
+        b2 = alphasur_peppho(2)
+        b3 = alphasur_peppho(3)
+        b4 = alphasur_peppho(4)
+        CALL sc_angular
        sqom1=om1*om1
        evdwij = 0.0d0
        ECL = 0.0d0
        sqom1=om1*om1
        evdwij = 0.0d0
        ECL = 0.0d0
@@ -25353,27 +25258,27 @@
        dGCLdOM12 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0
        dGCLdOM12 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0
-          Fcav = 0.0d0
-          dFdR = 0.0d0
-          dCAVdOM1  = 0.0d0
-          dCAVdOM2  = 0.0d0
-          dCAVdOM12 = 0.0d0
-          rij_shift = rij 
-          fac       = rij_shift**expon
-          c1        = fac  * fac * aa_peppho
+        Fcav = 0.0d0
+        dFdR = 0.0d0
+        dCAVdOM1  = 0.0d0
+        dCAVdOM2  = 0.0d0
+        dCAVdOM12 = 0.0d0
+        rij_shift = rij 
+        fac       = rij_shift**expon
+        c1        = fac  * fac * aa_peppho
 !          c1        = 0.0d0
 !          c1        = 0.0d0
-          c2        = fac  * bb_peppho
+        c2        = fac  * bb_peppho
 !          c2        = 0.0d0
 !          c2        = 0.0d0
-          evdwij    =  c1 + c2 
+        evdwij    =  c1 + c2 
 ! Now cavity....................
        eagle = dsqrt(1.0/rij_shift)
        top = b1 * ( eagle + b2 * 1.0/rij_shift - b3 )
 ! Now cavity....................
        eagle = dsqrt(1.0/rij_shift)
        top = b1 * ( eagle + b2 * 1.0/rij_shift - b3 )
-          bot = 1.0d0 + b4 * (1.0/rij_shift ** 12.0d0)
-          botsq = bot * bot
-          Fcav = top / bot
-          dtop = b1 * ((1.0/ (2.0d0 * eagle)) + (b2))
-          dbot = 12.0d0 * b4 * (1.0/rij_shift) ** 11.0d0
-          dFdR = ((dtop * bot - top * dbot) / botsq)
+        bot = 1.0d0 + b4 * (1.0/rij_shift ** 12.0d0)
+        botsq = bot * bot
+        Fcav = top / bot
+        dtop = b1 * ((1.0/ (2.0d0 * eagle)) + (b2))
+        dbot = 12.0d0 * b4 * (1.0/rij_shift) ** 11.0d0
+        dFdR = ((dtop * bot - top * dbot) / botsq)
        w1        = wqdip_peppho(1)
        w2        = wqdip_peppho(2)
 !       w1=0.0d0
        w1        = wqdip_peppho(1)
        w2        = wqdip_peppho(2)
 !       w1=0.0d0
@@ -25392,13 +25297,13 @@
        sparrow  = w1  *  om1
        hawk     = w2 *  (1.0d0 - sqom1)
        Ecl = sparrow * rij_shift**2.0d0 &
        sparrow  = w1  *  om1
        hawk     = w2 *  (1.0d0 - sqom1)
        Ecl = sparrow * rij_shift**2.0d0 &
-           - hawk    * rij_shift**4.0d0
+         - hawk    * rij_shift**4.0d0
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part
 !       rij_shift=5.0
        dGCLdR  = - 2.0d0 * sparrow * rij_shift**3.0d0 &
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part
 !       rij_shift=5.0
        dGCLdR  = - 2.0d0 * sparrow * rij_shift**3.0d0 &
-                + 4.0d0 * hawk    * rij_shift**5.0d0
+            + 4.0d0 * hawk    * rij_shift**5.0d0
 !c! dF/dom1
        dGCLdOM1 = (w1) * (rij_shift**2.0d0)
 !c! dF/dom2
 !c! dF/dom1
        dGCLdOM1 = (w1) * (rij_shift**2.0d0)
 !c! dF/dom2
@@ -25406,32 +25311,32 @@
        eom1  =    dGCLdOM1+dGCLdOM2 
        eom2  =    0.0               
        
        eom1  =    dGCLdOM1+dGCLdOM2 
        eom2  =    0.0               
        
-          fac    = -expon * (c1 + evdwij) * rij_shift+dFdR+dGCLdR 
+        fac    = -expon * (c1 + evdwij) * rij_shift+dFdR+dGCLdR 
 !          fac=0.0
 !          fac=0.0
-          gg(1) =  fac*xj*rij
-          gg(2) =  fac*yj*rij
-          gg(3) =  fac*zj*rij
-         do k=1,3
-         gvdwc_peppho(k,j) = gvdwc_peppho(k,j) +gg(k)/2.0
-         gvdwc_peppho(k,j+1) = gvdwc_peppho(k,j+1) +gg(k)/2.0
-         gvdwc_peppho(k,i) = gvdwc_peppho(k,i) -gg(k)/2.0
-         gvdwc_peppho(k,i+1) = gvdwc_peppho(k,i+1) -gg(k)/2.0
-         gg(k)=0.0
-         enddo
+        gg(1) =  fac*xj*rij
+        gg(2) =  fac*yj*rij
+        gg(3) =  fac*zj*rij
+       do k=1,3
+       gvdwc_peppho(k,j) = gvdwc_peppho(k,j) +gg(k)/2.0
+       gvdwc_peppho(k,j+1) = gvdwc_peppho(k,j+1) +gg(k)/2.0
+       gvdwc_peppho(k,i) = gvdwc_peppho(k,i) -gg(k)/2.0
+       gvdwc_peppho(k,i+1) = gvdwc_peppho(k,i+1) -gg(k)/2.0
+       gg(k)=0.0
+       enddo
 
       DO k = 1, 3
 
       DO k = 1, 3
-        dcosom1(k) = rij* (dc_norm(k,i) - om1 * erij(k))
-        dcosom2(k) = rij* (dc_norm(k,j) - om2 * erij(k))
-        gg(k) = gg(k) + eom1 * dcosom1(k)! + eom2 * dcosom2(k)
-        gvdwc_peppho(k,j)= gvdwc_peppho(k,j)        +0.5*( gg(k))   !&
+      dcosom1(k) = rij* (dc_norm(k,i) - om1 * erij(k))
+      dcosom2(k) = rij* (dc_norm(k,j) - om2 * erij(k))
+      gg(k) = gg(k) + eom1 * dcosom1(k)! + eom2 * dcosom2(k)
+      gvdwc_peppho(k,j)= gvdwc_peppho(k,j)        +0.5*( gg(k))   !&
 !                 - (eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv*2.0
 !                 - (eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv*2.0
-        gvdwc_peppho(k,j+1)= gvdwc_peppho(k,j+1)    +0.5*( gg(k))   !&
+      gvdwc_peppho(k,j+1)= gvdwc_peppho(k,j+1)    +0.5*( gg(k))   !&
 !                 + (eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv*2.0
 !                 + (eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv*2.0
-        gvdwc_peppho(k,i)= gvdwc_peppho(k,i)     -0.5*( gg(k))   &
-                 - (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
-        gvdwc_peppho(k,i+1)= gvdwc_peppho(k,i+1) - 0.5*( gg(k))  &
-                 + (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
-        enddo
+      gvdwc_peppho(k,i)= gvdwc_peppho(k,i)     -0.5*( gg(k))   &
+             - (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
+      gvdwc_peppho(k,i+1)= gvdwc_peppho(k,i+1) - 0.5*( gg(k))  &
+             + (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
+      enddo
        epeppho=epeppho+evdwij+Fcav+ECL
 !          print *,i,j,evdwij,Fcav,ECL,rij_shift
        enddo
        epeppho=epeppho+evdwij+Fcav+ECL
 !          print *,i,j,evdwij,Fcav,ECL,rij_shift
        enddo
@@ -25458,97 +25363,72 @@
 !el local variables
       integer :: iint,itypi1,subchap,isel
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,e1,e2,sigm,epsi
 !el local variables
       integer :: iint,itypi1,subchap,isel
       real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,e1,e2,sigm,epsi
-      real(kind=8) :: evdw
+      real(kind=8) :: evdw,aa,bb
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
-                    dist_temp, dist_init,ssgradlipi,ssgradlipj, &
-                    sslipi,sslipj,faclip,alpha_sco
+                dist_temp, dist_init,ssgradlipi,ssgradlipj, &
+                sslipi,sslipj,faclip,alpha_sco
       integer :: ii
       real(kind=8) :: fracinbuf
        real (kind=8) :: escpho
        real (kind=8),dimension(4):: ener
        real(kind=8) :: b1,b2,egb
        real(kind=8) :: Fisocav,ECL,Elj,Equad,Epol,eheadtail,&
       integer :: ii
       real(kind=8) :: fracinbuf
        real (kind=8) :: escpho
        real (kind=8),dimension(4):: ener
        real(kind=8) :: b1,b2,egb
        real(kind=8) :: Fisocav,ECL,Elj,Equad,Epol,eheadtail,&
-        Lambf,&
-        Chif,ChiLambf,Fcav,dFdR,dFdOM1,&
-        dFdOM2,dFdL,dFdOM12,&
-        federmaus,&
-        d1i,d1j
+      Lambf,&
+      Chif,ChiLambf,Fcav,dFdR,dFdOM1,&
+      dFdOM2,dFdL,dFdOM12,&
+      federmaus,&
+      d1i,d1j
 !       real(kind=8),dimension(3,2)::erhead_tail
 !       real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead,Rtail_distance
        real(kind=8) ::  facd4, adler, Fgb, facd3
        integer troll,jj,istate
        real (kind=8) :: dcosom1(3),dcosom2(3)
 !       real(kind=8),dimension(3,2)::erhead_tail
 !       real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead,Rtail_distance
        real(kind=8) ::  facd4, adler, Fgb, facd3
        integer troll,jj,istate
        real (kind=8) :: dcosom1(3),dcosom2(3)
+       evdw=0.0d0
        eps_out=80.0d0
        sss_ele_cut=1.0d0
 !       print *,"EVDW KURW",evdw,nres
       do i=iatsc_s,iatsc_e
 !        print *,"I am in EVDW",i
        eps_out=80.0d0
        sss_ele_cut=1.0d0
 !       print *,"EVDW KURW",evdw,nres
       do i=iatsc_s,iatsc_e
 !        print *,"I am in EVDW",i
-        itypi=iabs(itype(i,1))
+      itypi=iabs(itype(i,1))
 !        if (i.ne.47) cycle
 !        if (i.ne.47) cycle
-        if (itypi.eq.ntyp1) cycle
-        itypi1=iabs(itype(i+1,1))
-        xi=c(1,nres+i)
-        yi=c(2,nres+i)
-        zi=c(3,nres+i)
-          xi=dmod(xi,boxxsize)
-          if (xi.lt.0) xi=xi+boxxsize
-          yi=dmod(yi,boxysize)
-          if (yi.lt.0) yi=yi+boxysize
-          zi=dmod(zi,boxzsize)
-          if (zi.lt.0) zi=zi+boxzsize
-
-       if ((zi.gt.bordlipbot)  &
-        .and.(zi.lt.bordliptop)) then
-!C the energy transfer exist
-        if (zi.lt.buflipbot) then
-!C what fraction I am in
-         fracinbuf=1.0d0-  &
-              ((zi-bordlipbot)/lipbufthick)
-!C lipbufthick is thickenes of lipid buffore
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
-        elseif (zi.gt.bufliptop) then
-         fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
-         sslipi=sscalelip(fracinbuf)
-         ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
-        else
-         sslipi=1.0d0
-         ssgradlipi=0.0
-        endif
-       else
-         sslipi=0.0d0
-         ssgradlipi=0.0
-       endif
+      if (itypi.eq.ntyp1) cycle
+      itypi1=iabs(itype(i+1,1))
+      xi=c(1,nres+i)
+      yi=c(2,nres+i)
+      zi=c(3,nres+i)
+        call to_box(xi,yi,zi)
+        call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+!       endif
 !       print *, sslipi,ssgradlipi
 !       print *, sslipi,ssgradlipi
-        dxi=dc_norm(1,nres+i)
-        dyi=dc_norm(2,nres+i)
-        dzi=dc_norm(3,nres+i)
+      dxi=dc_norm(1,nres+i)
+      dyi=dc_norm(2,nres+i)
+      dzi=dc_norm(3,nres+i)
 !        dsci_inv=dsc_inv(itypi)
 !        dsci_inv=dsc_inv(itypi)
-        dsci_inv=vbld_inv(i+nres)
+      dsci_inv=vbld_inv(i+nres)
 !       write (iout,*) "i",i,dsc_inv(itypi),dsci_inv,1.0d0/vbld(i+nres)
 !       write (iout,*) "dcnori",dxi*dxi+dyi*dyi+dzi*dzi
 !
 ! Calculate SC interaction energy.
 !
 !       write (iout,*) "i",i,dsc_inv(itypi),dsci_inv,1.0d0/vbld(i+nres)
 !       write (iout,*) "dcnori",dxi*dxi+dyi*dyi+dzi*dzi
 !
 ! Calculate SC interaction energy.
 !
-        do iint=1,nint_gr(i)
-          do j=istart(i,iint),iend(i,iint)
+      do iint=1,nint_gr(i)
+        do j=istart(i,iint),iend(i,iint)
 !             print *,"JA PIER",i,j,iint,istart(i,iint),iend(i,iint)
 !             print *,"JA PIER",i,j,iint,istart(i,iint),iend(i,iint)
-            IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
-              call dyn_ssbond_ene(i,j,evdwij)
-              evdw=evdw+evdwij
-              if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') &
-                              'evdw',i,j,evdwij,' ss'
+          IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
+            call dyn_ssbond_ene(i,j,evdwij)
+            evdw=evdw+evdwij
+            if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') &
+                        'evdw',i,j,evdwij,' ss'
 !              if (energy_dec) write (iout,*) &
 !                              'evdw',i,j,evdwij,' ss'
 !              if (energy_dec) write (iout,*) &
 !                              'evdw',i,j,evdwij,' ss'
-             do k=j+1,iend(i,iint)
+           do k=j+1,iend(i,iint)
 !C search over all next residues
 !C search over all next residues
-              if (dyn_ss_mask(k)) then
+            if (dyn_ss_mask(k)) then
 !C check if they are cysteins
 !C              write(iout,*) 'k=',k
 
 !c              write(iout,*) "PRZED TRI", evdwij
 !               evdwij_przed_tri=evdwij
 !C check if they are cysteins
 !C              write(iout,*) 'k=',k
 
 !c              write(iout,*) "PRZED TRI", evdwij
 !               evdwij_przed_tri=evdwij
-              call triple_ssbond_ene(i,j,k,evdwij)
+            call triple_ssbond_ene(i,j,k,evdwij)
 !c               if(evdwij_przed_tri.ne.evdwij) then
 !c                 write (iout,*) "TRI:", evdwij, evdwij_przed_tri
 !c               endif
 !c               if(evdwij_przed_tri.ne.evdwij) then
 !c                 write (iout,*) "TRI:", evdwij, evdwij_przed_tri
 !c               endif
@@ -25556,64 +25436,36 @@
 !c              write(iout,*) "PO TRI", evdwij
 !C call the energy function that removes the artifical triple disulfide
 !C bond the soubroutine is located in ssMD.F
 !c              write(iout,*) "PO TRI", evdwij
 !C call the energy function that removes the artifical triple disulfide
 !C bond the soubroutine is located in ssMD.F
-              evdw=evdw+evdwij
-              if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') &
-                            'evdw',i,j,evdwij,'tss'
-              endif!dyn_ss_mask(k)
-             enddo! k
-            ELSE
+            evdw=evdw+evdwij
+            if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') &
+                      'evdw',i,j,evdwij,'tss'
+            endif!dyn_ss_mask(k)
+           enddo! k
+          ELSE
 !el            ind=ind+1
 !el            ind=ind+1
-            itypj=iabs(itype(j,1))
-            if (itypj.eq.ntyp1) cycle
-             CALL elgrad_init(eheadtail,Egb,Ecl,Elj,Equad,Epol)
+          itypj=iabs(itype(j,1))
+          if (itypj.eq.ntyp1) cycle
+           CALL elgrad_init(eheadtail,Egb,Ecl,Elj,Equad,Epol)
 
 !             if (j.ne.78) cycle
 !            dscj_inv=dsc_inv(itypj)
 
 !             if (j.ne.78) cycle
 !            dscj_inv=dsc_inv(itypj)
-            dscj_inv=vbld_inv(j+nres)
-           xj=c(1,j+nres)
-           yj=c(2,j+nres)
-           zj=c(3,j+nres)
-           xj=dmod(xj,boxxsize)
-           if (xj.lt.0) xj=xj+boxxsize
-           yj=dmod(yj,boxysize)
-           if (yj.lt.0) yj=yj+boxysize
-           zj=dmod(zj,boxzsize)
-           if (zj.lt.0) zj=zj+boxzsize
-          dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          xj_safe=xj
-          yj_safe=yj
-          zj_safe=zj
-          subchap=0
-
-          do xshift=-1,1
-          do yshift=-1,1
-          do zshift=-1,1
-          xj=xj_safe+xshift*boxxsize
-          yj=yj_safe+yshift*boxysize
-          zj=zj_safe+zshift*boxzsize
-          dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
-          if(dist_temp.lt.dist_init) then
-            dist_init=dist_temp
-            xj_temp=xj
-            yj_temp=yj
-            zj_temp=zj
-            subchap=1
-          endif
-          enddo
-          enddo
-          enddo
-          if (subchap.eq.1) then
-          xj=xj_temp-xi
-          yj=yj_temp-yi
-          zj=zj_temp-zi
-          else
-          xj=xj_safe-xi
-          yj=yj_safe-yi
-          zj=zj_safe-zi
-          endif
-          dxj = dc_norm( 1, nres+j )
-          dyj = dc_norm( 2, nres+j )
-          dzj = dc_norm( 3, nres+j )
+          dscj_inv=vbld_inv(j+nres)
+         xj=c(1,j+nres)
+         yj=c(2,j+nres)
+         zj=c(3,j+nres)
+     call to_box(xj,yj,zj)
+     call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+!      write(iout,*) "KRUWA", i,j
+      aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+      +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+      bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+      +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)
+        dxj = dc_norm( 1, nres+j )
+        dyj = dc_norm( 2, nres+j )
+        dzj = dc_norm( 3, nres+j )
 !          print *,i,j,itypi,itypj
 !          d1i=0.0d0
 !          d1j=0.0d0
 !          print *,i,j,itypi,itypj
 !          d1i=0.0d0
 !          d1j=0.0d0
@@ -25626,17 +25478,17 @@
 !          chip2=0.0d0
 ! not used by momo potential, but needed by sc_angular which is shared
 ! by all energy_potential subroutines
 !          chip2=0.0d0
 ! not used by momo potential, but needed by sc_angular which is shared
 ! by all energy_potential subroutines
-          alf1   = 0.0d0
-          alf2   = 0.0d0
-          alf12  = 0.0d0
-          a12sq = rborn(itypi,itypj) * rborn(itypj,itypi)
+        alf1   = 0.0d0
+        alf2   = 0.0d0
+        alf12  = 0.0d0
+        a12sq = rborn(itypi,itypj) * rborn(itypj,itypi)
 !       a12sq = a12sq * a12sq
 ! charge of amino acid itypi is...
 !       a12sq = a12sq * a12sq
 ! charge of amino acid itypi is...
-          chis1 = chis(itypi,itypj)
-          chis2 = chis(itypj,itypi)
-          chis12 = chis1 * chis2
-          sig1 = sigmap1(itypi,itypj)
-          sig2 = sigmap2(itypi,itypj)
+        chis1 = chis(itypi,itypj)
+        chis2 = chis(itypj,itypi)
+        chis12 = chis1 * chis2
+        sig1 = sigmap1(itypi,itypj)
+        sig2 = sigmap2(itypi,itypj)
 !       write (*,*) "sig1 = ", sig1
 !          chis1=0.0
 !          chis2=0.0
 !       write (*,*) "sig1 = ", sig1
 !          chis1=0.0
 !          chis2=0.0
@@ -25645,23 +25497,23 @@
 !          sig2=0.0
 !       write (*,*) "sig2 = ", sig2
 ! alpha factors from Fcav/Gcav
 !          sig2=0.0
 !       write (*,*) "sig2 = ", sig2
 ! alpha factors from Fcav/Gcav
-          b1cav = alphasur(1,itypi,itypj)
+        b1cav = alphasur(1,itypi,itypj)
 !          b1cav=0.0d0
 !          b1cav=0.0d0
-          b2cav = alphasur(2,itypi,itypj)
-          b3cav = alphasur(3,itypi,itypj)
-          b4cav = alphasur(4,itypi,itypj)
+        b2cav = alphasur(2,itypi,itypj)
+        b3cav = alphasur(3,itypi,itypj)
+        b4cav = alphasur(4,itypi,itypj)
 ! used to determine whether we want to do quadrupole calculations
        eps_in = epsintab(itypi,itypj)
        if (eps_in.eq.0.0) eps_in=1.0
 ! used to determine whether we want to do quadrupole calculations
        eps_in = epsintab(itypi,itypj)
        if (eps_in.eq.0.0) eps_in=1.0
-         
+       
        eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out))
        Rtail = 0.0d0
 !       dtail(1,itypi,itypj)=0.0
 !       dtail(2,itypi,itypj)=0.0
 
        DO k = 1, 3
        eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out))
        Rtail = 0.0d0
 !       dtail(1,itypi,itypj)=0.0
 !       dtail(2,itypi,itypj)=0.0
 
        DO k = 1, 3
-        ctail(k,1)=c(k,i+nres)-dtail(1,itypi,itypj)*dc_norm(k,nres+i)
-        ctail(k,2)=c(k,j+nres)-dtail(2,itypi,itypj)*dc_norm(k,nres+j)
+      ctail(k,1)=c(k,i+nres)-dtail(1,itypi,itypj)*dc_norm(k,nres+i)
+      ctail(k,2)=c(k,j+nres)-dtail(2,itypi,itypj)*dc_norm(k,nres+j)
        END DO
 !c! tail distances will be themselves usefull elswhere
 !c1 (in Gcav, for example)
        END DO
 !c! tail distances will be themselves usefull elswhere
 !c1 (in Gcav, for example)
@@ -25669,9 +25521,9 @@
        Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 )
        Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 )
        Rtail = dsqrt( &
        Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 )
        Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 )
        Rtail = dsqrt( &
-          (Rtail_distance(1)*Rtail_distance(1)) &
-        + (Rtail_distance(2)*Rtail_distance(2)) &
-        + (Rtail_distance(3)*Rtail_distance(3))) 
+        (Rtail_distance(1)*Rtail_distance(1)) &
+      + (Rtail_distance(2)*Rtail_distance(2)) &
+      + (Rtail_distance(3)*Rtail_distance(3))) 
 
 !       write (*,*) "eps_inout_fac = ", eps_inout_fac
 !-------------------------------------------------------------------
 
 !       write (*,*) "eps_inout_fac = ", eps_inout_fac
 !-------------------------------------------------------------------
@@ -25683,18 +25535,18 @@
 ! location of polar head is computed by taking hydrophobic centre
 ! and moving by a d1 * dc_norm vector
 ! see unres publications for very informative images
 ! location of polar head is computed by taking hydrophobic centre
 ! and moving by a d1 * dc_norm vector
 ! see unres publications for very informative images
-        chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
-        chead(k,2) = c(k, j+nres) + d2 * dc_norm(k, j+nres)
+      chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
+      chead(k,2) = c(k, j+nres) + d2 * dc_norm(k, j+nres)
 ! distance 
 !        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
 !        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
 ! distance 
 !        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
 !        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
-        Rhead_distance(k) = chead(k,2) - chead(k,1)
+      Rhead_distance(k) = chead(k,2) - chead(k,1)
        END DO
 ! pitagoras (root of sum of squares)
        Rhead = dsqrt( &
        END DO
 ! pitagoras (root of sum of squares)
        Rhead = dsqrt( &
-          (Rhead_distance(1)*Rhead_distance(1)) &
-        + (Rhead_distance(2)*Rhead_distance(2)) &
-        + (Rhead_distance(3)*Rhead_distance(3)))
+        (Rhead_distance(1)*Rhead_distance(1)) &
+      + (Rhead_distance(2)*Rhead_distance(2)) &
+      + (Rhead_distance(3)*Rhead_distance(3)))
 !-------------------------------------------------------------------
 ! zero everything that should be zero'ed
        evdwij = 0.0d0
 !-------------------------------------------------------------------
 ! zero everything that should be zero'ed
        evdwij = 0.0d0
@@ -25709,49 +25561,49 @@
        dGCLdOM12 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0
        dGCLdOM12 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0
-          Fcav = 0.0d0
-          dFdR = 0.0d0
-          dCAVdOM1  = 0.0d0
-          dCAVdOM2  = 0.0d0
-          dCAVdOM12 = 0.0d0
-          dscj_inv = vbld_inv(j+nres)
+        Fcav = 0.0d0
+        dFdR = 0.0d0
+        dCAVdOM1  = 0.0d0
+        dCAVdOM2  = 0.0d0
+        dCAVdOM12 = 0.0d0
+        dscj_inv = vbld_inv(j+nres)
 !          print *,i,j,dscj_inv,dsci_inv
 ! rij holds 1/(distance of Calpha atoms)
 !          print *,i,j,dscj_inv,dsci_inv
 ! rij holds 1/(distance of Calpha atoms)
-          rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
-          rij  = dsqrt(rrij)
+        rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
+        rij  = dsqrt(rrij)
 !----------------------------
 !----------------------------
-          CALL sc_angular
+        CALL sc_angular
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials
 ! om = omega, sqom = om^2
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials
 ! om = omega, sqom = om^2
-          sqom1  = om1 * om1
-          sqom2  = om2 * om2
-          sqom12 = om12 * om12
+        sqom1  = om1 * om1
+        sqom2  = om2 * om2
+        sqom12 = om12 * om12
 
 ! now we calculate EGB - Gey-Berne
 ! It will be summed up in evdwij and saved in evdw
 
 ! now we calculate EGB - Gey-Berne
 ! It will be summed up in evdwij and saved in evdw
-          sigsq     = 1.0D0  / sigsq
-          sig       = sig0ij * dsqrt(sigsq)
+        sigsq     = 1.0D0  / sigsq
+        sig       = sig0ij * dsqrt(sigsq)
 !          rij_shift = 1.0D0  / rij - sig + sig0ij
 !          rij_shift = 1.0D0  / rij - sig + sig0ij
-          rij_shift = Rtail - sig + sig0ij
-          IF (rij_shift.le.0.0D0) THEN
-           evdw = 1.0D20
-           RETURN
-          END IF
-          sigder = -sig * sigsq
-          rij_shift = 1.0D0 / rij_shift
-          fac       = rij_shift**expon
-          c1        = fac  * fac * aa_aq(itypi,itypj)
+        rij_shift = Rtail - sig + sig0ij
+        IF (rij_shift.le.0.0D0) THEN
+         evdw = 1.0D20
+         RETURN
+        END IF
+        sigder = -sig * sigsq
+        rij_shift = 1.0D0 / rij_shift
+        fac       = rij_shift**expon
+        c1        = fac  * fac * aa_aq(itypi,itypj)
 !          print *,"ADAM",aa_aq(itypi,itypj)
 
 !          c1        = 0.0d0
 !          print *,"ADAM",aa_aq(itypi,itypj)
 
 !          c1        = 0.0d0
-          c2        = fac  * bb_aq(itypi,itypj)
+        c2        = fac  * bb_aq(itypi,itypj)
 !          c2        = 0.0d0
 !          c2        = 0.0d0
-          evdwij    = eps1 * eps2rt * eps3rt * ( c1 + c2 )
-          eps2der   = eps3rt * evdwij
-          eps3der   = eps2rt * evdwij
+        evdwij    = eps1 * eps2rt * eps3rt * ( c1 + c2 )
+        eps2der   = eps3rt * evdwij
+        eps3der   = eps2rt * evdwij
 !          evdwij    = 4.0d0 * eps2rt * eps3rt * evdwij
 !          evdwij    = 4.0d0 * eps2rt * eps3rt * evdwij
-          evdwij    = eps2rt * eps3rt * evdwij
+        evdwij    = eps2rt * eps3rt * evdwij
 !#ifdef TSCSC
 !          IF (bb_aq(itypi,itypj).gt.0) THEN
 !           evdw_p = evdw_p + evdwij
 !#ifdef TSCSC
 !          IF (bb_aq(itypi,itypj).gt.0) THEN
 !           evdw_p = evdw_p + evdwij
@@ -25759,60 +25611,60 @@
 !           evdw_m = evdw_m + evdwij
 !          END IF
 !#else
 !           evdw_m = evdw_m + evdwij
 !          END IF
 !#else
-          evdw = evdw  &
-              + evdwij
+        evdw = evdw  &
+            + evdwij
 !#endif
 
 !#endif
 
-          c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
-          fac    = -expon * (c1 + evdwij) * rij_shift
-          sigder = fac * sigder
+        c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
+        fac    = -expon * (c1 + evdwij) * rij_shift
+        sigder = fac * sigder
 !          fac    = rij * fac
 ! Calculate distance derivative
 !          fac    = rij * fac
 ! Calculate distance derivative
-          gg(1) =  fac
-          gg(2) =  fac
-          gg(3) =  fac
+        gg(1) =  fac
+        gg(2) =  fac
+        gg(3) =  fac
 !          if (b2.gt.0.0) then
 !          if (b2.gt.0.0) then
-          fac = chis1 * sqom1 + chis2 * sqom2 &
-          - 2.0d0 * chis12 * om1 * om2 * om12
+        fac = chis1 * sqom1 + chis2 * sqom2 &
+        - 2.0d0 * chis12 * om1 * om2 * om12
 ! we will use pom later in Gcav, so dont mess with it!
 ! we will use pom later in Gcav, so dont mess with it!
-          pom = 1.0d0 - chis1 * chis2 * sqom12
-          Lambf = (1.0d0 - (fac / pom))
+        pom = 1.0d0 - chis1 * chis2 * sqom12
+        Lambf = (1.0d0 - (fac / pom))
 !          print *,"fac,pom",fac,pom,Lambf
 !          print *,"fac,pom",fac,pom,Lambf
-          Lambf = dsqrt(Lambf)
-          sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
+        Lambf = dsqrt(Lambf)
+        sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
 !          print *,"sig1,sig2",sig1,sig2,itypi,itypj
 !       write (*,*) "sparrow = ", sparrow
 !          print *,"sig1,sig2",sig1,sig2,itypi,itypj
 !       write (*,*) "sparrow = ", sparrow
-          Chif = Rtail * sparrow
+        Chif = Rtail * sparrow
 !           print *,"rij,sparrow",rij , sparrow 
 !           print *,"rij,sparrow",rij , sparrow 
-          ChiLambf = Chif * Lambf
-          eagle = dsqrt(ChiLambf)
-          bat = ChiLambf ** 11.0d0
-          top = b1cav * ( eagle + b2cav * ChiLambf - b3cav )
-          bot = 1.0d0 + b4cav * (ChiLambf ** 12.0d0)
-          botsq = bot * bot
+        ChiLambf = Chif * Lambf
+        eagle = dsqrt(ChiLambf)
+        bat = ChiLambf ** 11.0d0
+        top = b1cav * ( eagle + b2cav * ChiLambf - b3cav )
+        bot = 1.0d0 + b4cav * (ChiLambf ** 12.0d0)
+        botsq = bot * bot
 !          print *,top,bot,"bot,top",ChiLambf,Chif
 !          print *,top,bot,"bot,top",ChiLambf,Chif
-          Fcav = top / bot
+        Fcav = top / bot
 
        dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
        dbot = 12.0d0 * b4cav * bat * Lambf
        dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
 
 
        dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
        dbot = 12.0d0 * b4cav * bat * Lambf
        dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
 
-          dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
-          dbot = 12.0d0 * b4cav * bat * Chif
-          eagle = Lambf * pom
-          dFdOM1  = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
-          dFdOM2  = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
-          dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
-              * (chis2 * om2 * om12 - om1) / (eagle * pom)
+        dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
+        dbot = 12.0d0 * b4cav * bat * Chif
+        eagle = Lambf * pom
+        dFdOM1  = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
+        dFdOM2  = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
+        dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
+            * (chis2 * om2 * om12 - om1) / (eagle * pom)
 
 
-          dFdL = ((dtop * bot - top * dbot) / botsq)
+        dFdL = ((dtop * bot - top * dbot) / botsq)
 !       dFdL = 0.0d0
 !       dFdL = 0.0d0
-          dCAVdOM1  = dFdL * ( dFdOM1 )
-          dCAVdOM2  = dFdL * ( dFdOM2 )
-          dCAVdOM12 = dFdL * ( dFdOM12 )
+        dCAVdOM1  = dFdL * ( dFdOM1 )
+        dCAVdOM2  = dFdL * ( dFdOM2 )
+        dCAVdOM12 = dFdL * ( dFdOM12 )
 
        DO k= 1, 3
 
        DO k= 1, 3
-        ertail(k) = Rtail_distance(k)/Rtail
+      ertail(k) = Rtail_distance(k)/Rtail
        END DO
        erdxi = scalar( ertail(1), dC_norm(1,i+nres) )
        erdxj = scalar( ertail(1), dC_norm(1,j+nres) )
        END DO
        erdxi = scalar( ertail(1), dC_norm(1,i+nres) )
        erdxj = scalar( ertail(1), dC_norm(1,j+nres) )
@@ -25821,24 +25673,24 @@
        DO k = 1, 3
 !c!      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !c!      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
        DO k = 1, 3
 !c!      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !c!      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
-        pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
-        gvdwx(k,i) = gvdwx(k,i) &
-                  - (( dFdR + gg(k) ) * pom)
+      pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
+      gvdwx(k,i) = gvdwx(k,i) &
+              - (( dFdR + gg(k) ) * pom)
 !c!     &             - ( dFdR * pom )
 !c!     &             - ( dFdR * pom )
-        pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres))
-        gvdwx(k,j) = gvdwx(k,j)   &
-                  + (( dFdR + gg(k) ) * pom)
+      pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres))
+      gvdwx(k,j) = gvdwx(k,j)   &
+              + (( dFdR + gg(k) ) * pom)
 !c!     &             + ( dFdR * pom )
 
 !c!     &             + ( dFdR * pom )
 
-        gvdwc(k,i) = gvdwc(k,i)  &
-                  - (( dFdR + gg(k) ) * ertail(k))
+      gvdwc(k,i) = gvdwc(k,i)  &
+              - (( dFdR + gg(k) ) * ertail(k))
 !c!     &             - ( dFdR * ertail(k))
 
 !c!     &             - ( dFdR * ertail(k))
 
-        gvdwc(k,j) = gvdwc(k,j) &
-                  + (( dFdR + gg(k) ) * ertail(k))
+      gvdwc(k,j) = gvdwc(k,j) &
+              + (( dFdR + gg(k) ) * ertail(k))
 !c!     &             + ( dFdR * ertail(k))
 
 !c!     &             + ( dFdR * ertail(k))
 
-        gg(k) = 0.0d0
+      gg(k) = 0.0d0
 !      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
       END DO
 !      write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
 !      write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
       END DO
@@ -25846,7 +25698,7 @@
 
 !c! Compute head-head and head-tail energies for each state
 
 
 !c! Compute head-head and head-tail energies for each state
 
-          isel = iabs(Qi) + iabs(Qj)
+        isel = iabs(Qi) + iabs(Qj)
 ! double charge for Phophorylated! itype - 25,27,27
 !          if ((itype(i).eq.27).or.(itype(i).eq.26).or.(itype(i).eq.25)) then
 !            Qi=Qi*2
 ! double charge for Phophorylated! itype - 25,27,27
 !          if ((itype(i).eq.27).or.(itype(i).eq.26).or.(itype(i).eq.25)) then
 !            Qi=Qi*2
@@ -25858,123 +25710,123 @@
 !           endif
 
 !          isel=0
 !           endif
 
 !          isel=0
-          IF (isel.eq.0) THEN
+        IF (isel.eq.0) THEN
 !c! No charges - do nothing
 !c! No charges - do nothing
-           eheadtail = 0.0d0
+         eheadtail = 0.0d0
 
 
-          ELSE IF (isel.eq.4) THEN
+        ELSE IF (isel.eq.4) THEN
 !c! Calculate dipole-dipole interactions
 !c! Calculate dipole-dipole interactions
-           CALL edd(ecl)
-           eheadtail = ECL
+         CALL edd(ecl)
+         eheadtail = ECL
 !           eheadtail = 0.0d0
 
 !           eheadtail = 0.0d0
 
-          ELSE IF (isel.eq.1 .and. iabs(Qi).eq.1) THEN
+        ELSE IF (isel.eq.1 .and. iabs(Qi).eq.1) THEN
 !c! Charge-nonpolar interactions
 !c! Charge-nonpolar interactions
-          if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
-            Qi=Qi*2
-            Qij=Qij*2
-           endif
-          if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
-            Qj=Qj*2
-            Qij=Qij*2
-           endif
+        if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
+          Qi=Qi*2
+          Qij=Qij*2
+         endif
+        if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
+          Qj=Qj*2
+          Qij=Qij*2
+         endif
 
 
-           CALL eqn(epol)
-           eheadtail = epol
+         CALL eqn(epol)
+         eheadtail = epol
 !           eheadtail = 0.0d0
 
 !           eheadtail = 0.0d0
 
-          ELSE IF (isel.eq.1 .and. iabs(Qj).eq.1) THEN
+        ELSE IF (isel.eq.1 .and. iabs(Qj).eq.1) THEN
 !c! Nonpolar-charge interactions
 !c! Nonpolar-charge interactions
-          if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
-            Qi=Qi*2
-            Qij=Qij*2
-           endif
-          if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
-            Qj=Qj*2
-            Qij=Qij*2
-           endif
+        if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
+          Qi=Qi*2
+          Qij=Qij*2
+         endif
+        if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
+          Qj=Qj*2
+          Qij=Qij*2
+         endif
 
 
-           CALL enq(epol)
-           eheadtail = epol
+         CALL enq(epol)
+         eheadtail = epol
 !           eheadtail = 0.0d0
 
 !           eheadtail = 0.0d0
 
-          ELSE IF (isel.eq.3 .and. icharge(itypj).eq.2) THEN
+        ELSE IF (isel.eq.3 .and. icharge(itypj).eq.2) THEN
 !c! Charge-dipole interactions
 !c! Charge-dipole interactions
-          if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
-            Qi=Qi*2
-            Qij=Qij*2
-           endif
-          if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
-            Qj=Qj*2
-            Qij=Qij*2
-           endif
+        if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
+          Qi=Qi*2
+          Qij=Qij*2
+         endif
+        if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
+          Qj=Qj*2
+          Qij=Qij*2
+         endif
 
 
-           CALL eqd(ecl, elj, epol)
-           eheadtail = ECL + elj + epol
+         CALL eqd(ecl, elj, epol)
+         eheadtail = ECL + elj + epol
 !           eheadtail = 0.0d0
 
 !           eheadtail = 0.0d0
 
-          ELSE IF (isel.eq.3 .and. icharge(itypi).eq.2) THEN
+        ELSE IF (isel.eq.3 .and. icharge(itypi).eq.2) THEN
 !c! Dipole-charge interactions
 !c! Dipole-charge interactions
-          if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
-            Qi=Qi*2
-            Qij=Qij*2
-           endif
-          if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
-            Qj=Qj*2
-            Qij=Qij*2
-           endif
-           CALL edq(ecl, elj, epol)
-          eheadtail = ECL + elj + epol
+        if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
+          Qi=Qi*2
+          Qij=Qij*2
+         endif
+        if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
+          Qj=Qj*2
+          Qij=Qij*2
+         endif
+         CALL edq(ecl, elj, epol)
+        eheadtail = ECL + elj + epol
 !           eheadtail = 0.0d0
 
 !           eheadtail = 0.0d0
 
-          ELSE IF ((isel.eq.2.and.   &
-               iabs(Qi).eq.1).and.  &
-               nstate(itypi,itypj).eq.1) THEN
+        ELSE IF ((isel.eq.2.and.   &
+             iabs(Qi).eq.1).and.  &
+             nstate(itypi,itypj).eq.1) THEN
 !c! Same charge-charge interaction ( +/+ or -/- )
 !c! Same charge-charge interaction ( +/+ or -/- )
-          if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
-            Qi=Qi*2
-            Qij=Qij*2
-           endif
-          if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
-            Qj=Qj*2
-            Qij=Qij*2
-           endif
+        if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
+          Qi=Qi*2
+          Qij=Qij*2
+         endif
+        if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
+          Qj=Qj*2
+          Qij=Qij*2
+         endif
 
 
-           CALL eqq(Ecl,Egb,Epol,Fisocav,Elj)
-           eheadtail = ECL + Egb + Epol + Fisocav + Elj
+         CALL eqq(Ecl,Egb,Epol,Fisocav,Elj)
+         eheadtail = ECL + Egb + Epol + Fisocav + Elj
 !           eheadtail = 0.0d0
 
 !           eheadtail = 0.0d0
 
-          ELSE IF ((isel.eq.2.and.  &
-               iabs(Qi).eq.1).and. &
-               nstate(itypi,itypj).ne.1) THEN
+        ELSE IF ((isel.eq.2.and.  &
+             iabs(Qi).eq.1).and. &
+             nstate(itypi,itypj).ne.1) THEN
 !c! Different charge-charge interaction ( +/- or -/+ )
 !c! Different charge-charge interaction ( +/- or -/+ )
-          if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
-            Qi=Qi*2
-            Qij=Qij*2
-           endif
-          if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
-            Qj=Qj*2
-            Qij=Qij*2
-           endif
+        if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
+          Qi=Qi*2
+          Qij=Qij*2
+         endif
+        if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
+          Qj=Qj*2
+          Qij=Qij*2
+         endif
 
 
-           CALL energy_quad(istate,eheadtail,Ecl,Egb,Epol,Fisocav,Elj,Equad)
-          END IF
+         CALL energy_quad(istate,eheadtail,Ecl,Egb,Epol,Fisocav,Elj,Equad)
+        END IF
        END IF  ! this endif ends the "catch the gly-gly" at the beggining of Fcav
       evdw = evdw  + Fcav + eheadtail
 
        IF (energy_dec) write (iout,'(2(1x,a3,i3),3f6.2,10f16.7)') &
        END IF  ! this endif ends the "catch the gly-gly" at the beggining of Fcav
       evdw = evdw  + Fcav + eheadtail
 
        IF (energy_dec) write (iout,'(2(1x,a3,i3),3f6.2,10f16.7)') &
-        restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
-        1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
-        Equad,evdwij+Fcav+eheadtail,evdw
+      restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
+      1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
+      Equad,evdwij+Fcav+eheadtail,evdw
 !       evdw = evdw  + Fcav  + eheadtail
 
 !       evdw = evdw  + Fcav  + eheadtail
 
-        iF (nstate(itypi,itypj).eq.1) THEN
-        CALL sc_grad
+      iF (nstate(itypi,itypj).eq.1) THEN
+      CALL sc_grad
        END IF
 !c!-------------------------------------------------------------------
 !c! NAPISY KONCOWE
        END IF
 !c!-------------------------------------------------------------------
 !c! NAPISY KONCOWE
-         END DO   ! j
-        END DO    ! iint
+       END DO   ! j
+      END DO    ! iint
        END DO     ! i
 !c      write (iout,*) "Number of loop steps in EGB:",ind
 !c      energy_dec=.false.
        END DO     ! i
 !c      write (iout,*) "Number of loop steps in EGB:",ind
 !c      energy_dec=.false.
@@ -25987,7 +25839,7 @@
       use calc_data
       use comm_momo
        real (kind=8) ::  facd3, facd4, federmaus, adler,&
       use calc_data
       use comm_momo
        real (kind=8) ::  facd3, facd4, federmaus, adler,&
-         Ecl,Egb,Epol,Fisocav,Elj,Fgb,debkap
+       Ecl,Egb,Epol,Fisocav,Elj,Fgb,debkap
 !       integer :: k
 !c! Epol and Gpol analytical parameters
        alphapol1 = alphapol(itypi,itypj)
 !       integer :: k
 !c! Epol and Gpol analytical parameters
        alphapol1 = alphapol(itypi,itypj)
@@ -25998,8 +25850,8 @@
        al3  = alphiso(3,itypi,itypj)
        al4  = alphiso(4,itypi,itypj)
        csig = (1.0d0  &
        al3  = alphiso(3,itypi,itypj)
        al4  = alphiso(4,itypi,itypj)
        csig = (1.0d0  &
-           / dsqrt(sigiso1(itypi, itypj)**2.0d0 &
-           + sigiso2(itypi,itypj)**2.0d0))
+         / dsqrt(sigiso1(itypi, itypj)**2.0d0 &
+         + sigiso2(itypi,itypj)**2.0d0))
 !c!
        pis  = sig0head(itypi,itypj)
        eps_head = epshead(itypi,itypj)
 !c!
        pis  = sig0head(itypi,itypj)
        eps_head = epshead(itypi,itypj)
@@ -26010,8 +25862,8 @@
        R2 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances needed by Epol
        R2 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances needed by Epol
-        R1=R1+(ctail(k,2)-chead(k,1))**2
-        R2=R2+(chead(k,2)-ctail(k,1))**2
+      R1=R1+(ctail(k,2)-chead(k,1))**2
+      R2=R2+(chead(k,2)-ctail(k,1))**2
        END DO
 !c! Pitagoras
        R1 = dsqrt(R1)
        END DO
 !c! Pitagoras
        R1 = dsqrt(R1)
@@ -26034,13 +25886,13 @@
        Fgb = sqrt( ( Rhead_sq ) + a12sq * ee0)
        debkap=debaykap(itypi,itypj)
        Egb = -(332.0d0 * Qij *&
        Fgb = sqrt( ( Rhead_sq ) + a12sq * ee0)
        debkap=debaykap(itypi,itypj)
        Egb = -(332.0d0 * Qij *&
-        (1.0/eps_in-dexp(-debkap*Fgb)/eps_out)) / Fgb
+      (1.0/eps_in-dexp(-debkap*Fgb)/eps_out)) / Fgb
 !       print *,"EGB WTF",Qij,eps_inout_fac,Fgb,itypi,itypj,eps_in,eps_out
 !c! Derivative of Egb is Ggb...
        dGGBdFGB = -(-332.0d0 * Qij * &
        (1.0/eps_in-dexp(-debkap*Fgb)/eps_out))/(Fgb*Fgb)&
        -(332.0d0 * Qij *&
 !       print *,"EGB WTF",Qij,eps_inout_fac,Fgb,itypi,itypj,eps_in,eps_out
 !c! Derivative of Egb is Ggb...
        dGGBdFGB = -(-332.0d0 * Qij * &
        (1.0/eps_in-dexp(-debkap*Fgb)/eps_out))/(Fgb*Fgb)&
        -(332.0d0 * Qij *&
-        (dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb
+      (dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb
        dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb )
        dGGBdR = dGGBdFGB * dFGBdR
 !c!-------------------------------------------------------------------
        dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb )
        dGGBdR = dGGBdFGB * dFGBdR
 !c!-------------------------------------------------------------------
@@ -26079,17 +25931,17 @@
       (( alphapol1 / fgb1 )**4.0d0)+((alphapol2/fgb2) ** 4.0d0 ))
 !c!       epol = 0.0d0
        dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0)&
       (( alphapol1 / fgb1 )**4.0d0)+((alphapol2/fgb2) ** 4.0d0 ))
 !c!       epol = 0.0d0
        dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0)&
-               / (fgb1 ** 5.0d0)
+             / (fgb1 ** 5.0d0)
        dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0)&
        dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0)&
-               / (fgb2 ** 5.0d0)
+             / (fgb2 ** 5.0d0)
        dFGBdR1 = ( (R1 / MomoFac1)* ( 2.0d0 - (0.5d0 * ee1) ) )&
        dFGBdR1 = ( (R1 / MomoFac1)* ( 2.0d0 - (0.5d0 * ee1) ) )&
-             / ( 2.0d0 * fgb1 )
+           / ( 2.0d0 * fgb1 )
        dFGBdR2 = ( (R2 / MomoFac2)* ( 2.0d0 - (0.5d0 * ee2) ) )&
        dFGBdR2 = ( (R2 / MomoFac2)* ( 2.0d0 - (0.5d0 * ee2) ) )&
-             / ( 2.0d0 * fgb2 )
+           / ( 2.0d0 * fgb2 )
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1))&
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1))&
-                * ( 2.0d0 - 0.5d0 * ee1) ) / ( 2.0d0 * fgb1 )
+            * ( 2.0d0 - 0.5d0 * ee1) ) / ( 2.0d0 * fgb1 )
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))&
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))&
-                * ( 2.0d0 - 0.5d0 * ee2) ) / ( 2.0d0 * fgb2 )
+            * ( 2.0d0 - 0.5d0 * ee2) ) / ( 2.0d0 * fgb2 )
        dPOLdR1 = dPOLdFGB1 * dFGBdR1
 !c!       dPOLdR1 = 0.0d0
        dPOLdR2 = dPOLdFGB2 * dFGBdR2
        dPOLdR1 = dPOLdFGB1 * dFGBdR1
 !c!       dPOLdR1 = 0.0d0
        dPOLdR2 = dPOLdFGB2 * dFGBdR2
@@ -26105,7 +25957,7 @@
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))&
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))&
-             +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+           +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! These things do the dRdX derivatives, that is
 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! These things do the dRdX derivatives, that is
@@ -26113,9 +25965,9 @@
 !c! distance to function that changes with LOCATION (of the interaction
 !c! site)
        DO k = 1, 3
 !c! distance to function that changes with LOCATION (of the interaction
 !c! site)
        DO k = 1, 3
-        erhead(k) = Rhead_distance(k)/Rhead
-        erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
-        erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+      erhead(k) = Rhead_distance(k)/Rhead
+      erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
+      erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
        END DO
 
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
        END DO
 
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
@@ -26131,43 +25983,43 @@
 
 !c! Now we add appropriate partial derivatives (one in each dimension)
        DO k = 1, 3
 
 !c! Now we add appropriate partial derivatives (one in each dimension)
        DO k = 1, 3
-        hawk   = (erhead_tail(k,1) + &
-        facd1 * (erhead_tail(k,1) - bat   * dC_norm(k,i+nres)))
-        condor = (erhead_tail(k,2) + &
-        facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres)))
-
-        pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
-        gvdwx(k,i) = gvdwx(k,i) &
-                  - dGCLdR * pom&
-                  - dGGBdR * pom&
-                  - dGCVdR * pom&
-                  - dPOLdR1 * hawk&
-                  - dPOLdR2 * (erhead_tail(k,2)&
+      hawk   = (erhead_tail(k,1) + &
+      facd1 * (erhead_tail(k,1) - bat   * dC_norm(k,i+nres)))
+      condor = (erhead_tail(k,2) + &
+      facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres)))
+
+      pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+      gvdwx(k,i) = gvdwx(k,i) &
+              - dGCLdR * pom&
+              - dGGBdR * pom&
+              - dGCVdR * pom&
+              - dPOLdR1 * hawk&
+              - dPOLdR2 * (erhead_tail(k,2)&
       -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))&
       -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))&
-                  - dGLJdR * pom
+              - dGLJdR * pom
 
 
-        pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
-        gvdwx(k,j) = gvdwx(k,j)+ dGCLdR * pom&
-                   + dGGBdR * pom+ dGCVdR * pom&
-                  + dPOLdR1 * (erhead_tail(k,1)&
+      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+      gvdwx(k,j) = gvdwx(k,j)+ dGCLdR * pom&
+               + dGGBdR * pom+ dGCVdR * pom&
+              + dPOLdR1 * (erhead_tail(k,1)&
       -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres)))&
       -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres)))&
-                  + dPOLdR2 * condor + dGLJdR * pom
-
-        gvdwc(k,i) = gvdwc(k,i)  &
-                  - dGCLdR * erhead(k)&
-                  - dGGBdR * erhead(k)&
-                  - dGCVdR * erhead(k)&
-                  - dPOLdR1 * erhead_tail(k,1)&
-                  - dPOLdR2 * erhead_tail(k,2)&
-                  - dGLJdR * erhead(k)
-
-        gvdwc(k,j) = gvdwc(k,j)         &
-                  + dGCLdR * erhead(k) &
-                  + dGGBdR * erhead(k) &
-                  + dGCVdR * erhead(k) &
-                  + dPOLdR1 * erhead_tail(k,1) &
-                  + dPOLdR2 * erhead_tail(k,2)&
-                  + dGLJdR * erhead(k)
+              + dPOLdR2 * condor + dGLJdR * pom
+
+      gvdwc(k,i) = gvdwc(k,i)  &
+              - dGCLdR * erhead(k)&
+              - dGGBdR * erhead(k)&
+              - dGCVdR * erhead(k)&
+              - dPOLdR1 * erhead_tail(k,1)&
+              - dPOLdR2 * erhead_tail(k,2)&
+              - dGLJdR * erhead(k)
+
+      gvdwc(k,j) = gvdwc(k,j)         &
+              + dGCLdR * erhead(k) &
+              + dGGBdR * erhead(k) &
+              + dGCVdR * erhead(k) &
+              + dPOLdR1 * erhead_tail(k,1) &
+              + dPOLdR2 * erhead_tail(k,2)&
+              + dGLJdR * erhead(k)
 
        END DO
        RETURN
 
        END DO
        RETURN
@@ -26177,19 +26029,19 @@
       use calc_data
       use comm_momo
        real (kind=8) ::  facd3, facd4, federmaus, adler,&
       use calc_data
       use comm_momo
        real (kind=8) ::  facd3, facd4, federmaus, adler,&
-         Ecl,Egb,Epol,Fisocav,Elj,Fgb,debkap
+       Ecl,Egb,Epol,Fisocav,Elj,Fgb,debkap
 !       integer :: k
 !c! Epol and Gpol analytical parameters
        alphapol1 = alphapolcat(itypi,itypj)
 !       integer :: k
 !c! Epol and Gpol analytical parameters
        alphapol1 = alphapolcat(itypi,itypj)
-       alphapol2 = alphapolcat(itypj,itypi)
+       alphapol2 = alphapolcat2(itypj,itypi)
 !c! Fisocav and Gisocav analytical parameters
        al1  = alphisocat(1,itypi,itypj)
        al2  = alphisocat(2,itypi,itypj)
        al3  = alphisocat(3,itypi,itypj)
        al4  = alphisocat(4,itypi,itypj)
        csig = (1.0d0  &
 !c! Fisocav and Gisocav analytical parameters
        al1  = alphisocat(1,itypi,itypj)
        al2  = alphisocat(2,itypi,itypj)
        al3  = alphisocat(3,itypi,itypj)
        al4  = alphisocat(4,itypi,itypj)
        csig = (1.0d0  &
-           / dsqrt(sigiso1cat(itypi, itypj)**2.0d0 &
-           + sigiso2cat(itypi,itypj)**2.0d0))
+         / dsqrt(sigiso1cat(itypi, itypj)**2.0d0 &
+         + sigiso2cat(itypi,itypj)**2.0d0))
 !c!
        pis  = sig0headcat(itypi,itypj)
        eps_head = epsheadcat(itypi,itypj)
 !c!
        pis  = sig0headcat(itypi,itypj)
        eps_head = epsheadcat(itypi,itypj)
@@ -26200,8 +26052,8 @@
        R2 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances needed by Epol
        R2 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances needed by Epol
-        R1=R1+(ctail(k,2)-chead(k,1))**2
-        R2=R2+(chead(k,2)-ctail(k,1))**2
+      R1=R1+(ctail(k,2)-chead(k,1))**2
+      R2=R2+(chead(k,2)-ctail(k,1))**2
        END DO
 !c! Pitagoras
        R1 = dsqrt(R1)
        END DO
 !c! Pitagoras
        R1 = dsqrt(R1)
@@ -26224,13 +26076,13 @@
        Fgb = sqrt( ( Rhead_sq ) + a12sq * ee0)
        debkap=debaykapcat(itypi,itypj)
        Egb = -(332.0d0 * Qij *&
        Fgb = sqrt( ( Rhead_sq ) + a12sq * ee0)
        debkap=debaykapcat(itypi,itypj)
        Egb = -(332.0d0 * Qij *&
-        (1.0/eps_in-dexp(-debkap*Fgb)/eps_out)) / Fgb
+      (1.0/eps_in-dexp(-debkap*Fgb)/eps_out)) / Fgb
 !       print *,"EGB WTF",Qij,eps_inout_fac,Fgb,itypi,itypj,eps_in,eps_out
 !c! Derivative of Egb is Ggb...
        dGGBdFGB = -(-332.0d0 * Qij * &
        (1.0/eps_in-dexp(-debkap*Fgb)/eps_out))/(Fgb*Fgb)&
        -(332.0d0 * Qij *&
 !       print *,"EGB WTF",Qij,eps_inout_fac,Fgb,itypi,itypj,eps_in,eps_out
 !c! Derivative of Egb is Ggb...
        dGGBdFGB = -(-332.0d0 * Qij * &
        (1.0/eps_in-dexp(-debkap*Fgb)/eps_out))/(Fgb*Fgb)&
        -(332.0d0 * Qij *&
-        (dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb
+      (dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb
        dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb )
        dGGBdR = dGGBdFGB * dFGBdR
 !c!-------------------------------------------------------------------
        dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb )
        dGGBdR = dGGBdFGB * dFGBdR
 !c!-------------------------------------------------------------------
@@ -26269,17 +26121,17 @@
       (( alphapol1 / fgb1 )**4.0d0)+((alphapol2/fgb2) ** 4.0d0 ))
 !c!       epol = 0.0d0
        dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0)&
       (( alphapol1 / fgb1 )**4.0d0)+((alphapol2/fgb2) ** 4.0d0 ))
 !c!       epol = 0.0d0
        dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0)&
-               / (fgb1 ** 5.0d0)
+             / (fgb1 ** 5.0d0)
        dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0)&
        dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0)&
-               / (fgb2 ** 5.0d0)
+             / (fgb2 ** 5.0d0)
        dFGBdR1 = ( (R1 / MomoFac1)* ( 2.0d0 - (0.5d0 * ee1) ) )&
        dFGBdR1 = ( (R1 / MomoFac1)* ( 2.0d0 - (0.5d0 * ee1) ) )&
-             / ( 2.0d0 * fgb1 )
+           / ( 2.0d0 * fgb1 )
        dFGBdR2 = ( (R2 / MomoFac2)* ( 2.0d0 - (0.5d0 * ee2) ) )&
        dFGBdR2 = ( (R2 / MomoFac2)* ( 2.0d0 - (0.5d0 * ee2) ) )&
-             / ( 2.0d0 * fgb2 )
+           / ( 2.0d0 * fgb2 )
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1))&
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1))&
-                * ( 2.0d0 - 0.5d0 * ee1) ) / ( 2.0d0 * fgb1 )
+            * ( 2.0d0 - 0.5d0 * ee1) ) / ( 2.0d0 * fgb1 )
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))&
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))&
-                * ( 2.0d0 - 0.5d0 * ee2) ) / ( 2.0d0 * fgb2 )
+            * ( 2.0d0 - 0.5d0 * ee2) ) / ( 2.0d0 * fgb2 )
        dPOLdR1 = dPOLdFGB1 * dFGBdR1
 !c!       dPOLdR1 = 0.0d0
        dPOLdR2 = dPOLdFGB2 * dFGBdR2
        dPOLdR1 = dPOLdFGB1 * dFGBdR1
 !c!       dPOLdR1 = 0.0d0
        dPOLdR2 = dPOLdFGB2 * dFGBdR2
@@ -26295,7 +26147,7 @@
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))&
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))&
-             +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+           +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! These things do the dRdX derivatives, that is
 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! These things do the dRdX derivatives, that is
@@ -26303,9 +26155,9 @@
 !c! distance to function that changes with LOCATION (of the interaction
 !c! site)
        DO k = 1, 3
 !c! distance to function that changes with LOCATION (of the interaction
 !c! site)
        DO k = 1, 3
-        erhead(k) = Rhead_distance(k)/Rhead
-        erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
-        erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+      erhead(k) = Rhead_distance(k)/Rhead
+      erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
+      erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
        END DO
 
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
        END DO
 
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
@@ -26321,43 +26173,43 @@
 
 !c! Now we add appropriate partial derivatives (one in each dimension)
        DO k = 1, 3
 
 !c! Now we add appropriate partial derivatives (one in each dimension)
        DO k = 1, 3
-        hawk   = (erhead_tail(k,1) + &
-        facd1 * (erhead_tail(k,1) - bat   * dC_norm(k,i+nres)))
-        condor = (erhead_tail(k,2) + &
-        facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j)))
-
-        pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
-        gvdwx(k,i) = gvdwx(k,i) &
-                  - dGCLdR * pom&
-                  - dGGBdR * pom&
-                  - dGCVdR * pom&
-                  - dPOLdR1 * hawk&
-                  - dPOLdR2 * (erhead_tail(k,2)&
+      hawk   = (erhead_tail(k,1) + &
+      facd1 * (erhead_tail(k,1) - bat   * dC_norm(k,i+nres)))
+      condor = (erhead_tail(k,2) + &
+      facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j)))
+
+      pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+      gradpepcatx(k,i) = gradpepcatx(k,i) &
+              - dGCLdR * pom&
+              - dGGBdR * pom&
+              - dGCVdR * pom&
+              - dPOLdR1 * hawk&
+              - dPOLdR2 * (erhead_tail(k,2)&
       -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))&
       -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))&
-                  - dGLJdR * pom
-
-        pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j))
-        gvdwx(k,j) = gvdwx(k,j)+ dGCLdR * pom&
-                   + dGGBdR * pom+ dGCVdR * pom&
-                  + dPOLdR1 * (erhead_tail(k,1)&
-      -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j)))&
-                  + dPOLdR2 * condor + dGLJdR * pom
-
-        gvdwc(k,i) = gvdwc(k,i)  &
-                  - dGCLdR * erhead(k)&
-                  - dGGBdR * erhead(k)&
-                  - dGCVdR * erhead(k)&
-                  - dPOLdR1 * erhead_tail(k,1)&
-                  - dPOLdR2 * erhead_tail(k,2)&
-                  - dGLJdR * erhead(k)
-
-        gvdwc(k,j) = gvdwc(k,j)         &
-                  + dGCLdR * erhead(k) &
-                  + dGGBdR * erhead(k) &
-                  + dGCVdR * erhead(k) &
-                  + dPOLdR1 * erhead_tail(k,1) &
-                  + dPOLdR2 * erhead_tail(k,2)&
-                  + dGLJdR * erhead(k)
+              - dGLJdR * pom
+
+      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j))
+!        gradpepcatx(k,j) = gradpepcatx(k,j)+ dGCLdR * pom&
+!                   + dGGBdR * pom+ dGCVdR * pom&
+!                  + dPOLdR1 * (erhead_tail(k,1)&
+!      -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j)))&
+!                  + dPOLdR2 * condor + dGLJdR * pom
+
+      gradpepcat(k,i) = gradpepcat(k,i)  &
+              - dGCLdR * erhead(k)&
+              - dGGBdR * erhead(k)&
+              - dGCVdR * erhead(k)&
+              - dPOLdR1 * erhead_tail(k,1)&
+              - dPOLdR2 * erhead_tail(k,2)&
+              - dGLJdR * erhead(k)
+
+      gradpepcat(k,j) = gradpepcat(k,j)         &
+              + dGCLdR * erhead(k) &
+              + dGGBdR * erhead(k) &
+              + dGCVdR * erhead(k) &
+              + dPOLdR1 * erhead_tail(k,1) &
+              + dPOLdR2 * erhead_tail(k,2)&
+              + dGLJdR * erhead(k)
 
        END DO
        RETURN
 
        END DO
        RETURN
@@ -26385,7 +26237,7 @@
        al3  = alphiso(3,itypi,itypj)
        al4  = alphiso(4,itypi,itypj)
        csig = (1.0d0 / dsqrt(sigiso1(itypi, itypj)**2.0d0&
        al3  = alphiso(3,itypi,itypj)
        al4  = alphiso(4,itypi,itypj)
        csig = (1.0d0 / dsqrt(sigiso1(itypi, itypj)**2.0d0&
-            + sigiso2(itypi,itypj)**2.0d0))
+          + sigiso2(itypi,itypj)**2.0d0))
 !c!
        w1   = wqdip(1,itypi,itypj)
        w2   = wqdip(2,itypi,itypj)
 !c!
        w1   = wqdip(1,itypi,itypj)
        w2   = wqdip(2,itypi,itypj)
@@ -26394,34 +26246,34 @@
 !c! First things first:
 !c! We need to do sc_grad's job with GB and Fcav
        eom1  = eps2der * eps2rt_om1 &
 !c! First things first:
 !c! We need to do sc_grad's job with GB and Fcav
        eom1  = eps2der * eps2rt_om1 &
-             - 2.0D0 * alf1 * eps3der&
-             + sigder * sigsq_om1&
-             + dCAVdOM1
+           - 2.0D0 * alf1 * eps3der&
+           + sigder * sigsq_om1&
+           + dCAVdOM1
        eom2  = eps2der * eps2rt_om2 &
        eom2  = eps2der * eps2rt_om2 &
-             + 2.0D0 * alf2 * eps3der&
-             + sigder * sigsq_om2&
-             + dCAVdOM2
+           + 2.0D0 * alf2 * eps3der&
+           + sigder * sigsq_om2&
+           + dCAVdOM2
        eom12 =  evdwij  * eps1_om12 &
        eom12 =  evdwij  * eps1_om12 &
-             + eps2der * eps2rt_om12 &
-             - 2.0D0 * alf12 * eps3der&
-             + sigder *sigsq_om12&
-             + dCAVdOM12
+           + eps2der * eps2rt_om12 &
+           - 2.0D0 * alf12 * eps3der&
+           + sigder *sigsq_om12&
+           + dCAVdOM12
 !c! now some magical transformations to project gradient into
 !c! three cartesian vectors
        DO k = 1, 3
 !c! now some magical transformations to project gradient into
 !c! three cartesian vectors
        DO k = 1, 3
-        dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k))
-        dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
-        gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
+      dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k))
+      dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
+      gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
 !c! this acts on hydrophobic center of interaction
 !c! this acts on hydrophobic center of interaction
-        gvdwx(k,i)= gvdwx(k,i) - gg(k) &
-                  + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))&
-                  + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
-        gvdwx(k,j)= gvdwx(k,j) + gg(k) &
-                  + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))&
-                  + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+      gvdwx(k,i)= gvdwx(k,i) - gg(k) &
+              + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))&
+              + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+      gvdwx(k,j)= gvdwx(k,j) + gg(k) &
+              + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))&
+              + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
 !c! this acts on Calpha
 !c! this acts on Calpha
-        gvdwc(k,i)=gvdwc(k,i)-gg(k)
-        gvdwc(k,j)=gvdwc(k,j)+gg(k)
+      gvdwc(k,i)=gvdwc(k,i)-gg(k)
+      gvdwc(k,j)=gvdwc(k,j)+gg(k)
        END DO
 !c! sc_grad is done, now we will compute 
        eheadtail = 0.0d0
        END DO
 !c! sc_grad is done, now we will compute 
        eheadtail = 0.0d0
@@ -26430,54 +26282,54 @@
        eom12 = 0.0d0
        DO istate = 1, nstate(itypi,itypj)
 !c*************************************************************
        eom12 = 0.0d0
        DO istate = 1, nstate(itypi,itypj)
 !c*************************************************************
-        IF (istate.ne.1) THEN
-         IF (istate.lt.3) THEN
-          ii = 1
-         ELSE
-          ii = 2
-         END IF
-        jj = istate/ii
-        d1 = dhead(1,ii,itypi,itypj)
-        d2 = dhead(2,jj,itypi,itypj)
-        DO k = 1,3
-         chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
-         chead(k,2) = c(k, j+nres) + d2 * dc_norm(k, j+nres)
-         Rhead_distance(k) = chead(k,2) - chead(k,1)
-        END DO
+      IF (istate.ne.1) THEN
+       IF (istate.lt.3) THEN
+        ii = 1
+       ELSE
+        ii = 2
+       END IF
+      jj = istate/ii
+      d1 = dhead(1,ii,itypi,itypj)
+      d2 = dhead(2,jj,itypi,itypj)
+      DO k = 1,3
+       chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
+       chead(k,2) = c(k, j+nres) + d2 * dc_norm(k, j+nres)
+       Rhead_distance(k) = chead(k,2) - chead(k,1)
+      END DO
 !c! pitagoras (root of sum of squares)
 !c! pitagoras (root of sum of squares)
-        Rhead = dsqrt( &
-               (Rhead_distance(1)*Rhead_distance(1))  &
-             + (Rhead_distance(2)*Rhead_distance(2))  &
-             + (Rhead_distance(3)*Rhead_distance(3))) 
-        END IF
-        Rhead_sq = Rhead * Rhead
+      Rhead = dsqrt( &
+             (Rhead_distance(1)*Rhead_distance(1))  &
+           + (Rhead_distance(2)*Rhead_distance(2))  &
+           + (Rhead_distance(3)*Rhead_distance(3))) 
+      END IF
+      Rhead_sq = Rhead * Rhead
 
 !c! R1 - distance between head of ith side chain and tail of jth sidechain
 !c! R2 - distance between head of jth side chain and tail of ith sidechain
 
 !c! R1 - distance between head of ith side chain and tail of jth sidechain
 !c! R2 - distance between head of jth side chain and tail of ith sidechain
-        R1 = 0.0d0
-        R2 = 0.0d0
-        DO k = 1, 3
+      R1 = 0.0d0
+      R2 = 0.0d0
+      DO k = 1, 3
 !c! Calculate head-to-tail distances
 !c! Calculate head-to-tail distances
-         R1=R1+(ctail(k,2)-chead(k,1))**2
-         R2=R2+(chead(k,2)-ctail(k,1))**2
-        END DO
+       R1=R1+(ctail(k,2)-chead(k,1))**2
+       R2=R2+(chead(k,2)-ctail(k,1))**2
+      END DO
 !c! Pitagoras
 !c! Pitagoras
-        R1 = dsqrt(R1)
-        R2 = dsqrt(R2)
-        Ecl = (332.0d0 * Qij) / (Rhead * eps_in)
+      R1 = dsqrt(R1)
+      R2 = dsqrt(R2)
+      Ecl = (332.0d0 * Qij) / (Rhead * eps_in)
 !c!        Ecl = 0.0d0
 !c!        write (*,*) "Ecl = ", Ecl
 !c! derivative of Ecl is Gcl...
 !c!        Ecl = 0.0d0
 !c!        write (*,*) "Ecl = ", Ecl
 !c! derivative of Ecl is Gcl...
-        dGCLdR = (-332.0d0 * Qij ) / (Rhead_sq * eps_in)
+      dGCLdR = (-332.0d0 * Qij ) / (Rhead_sq * eps_in)
 !c!        dGCLdR = 0.0d0
 !c!        dGCLdR = 0.0d0
-        dGCLdOM1 = 0.0d0
-        dGCLdOM2 = 0.0d0
-        dGCLdOM12 = 0.0d0
+      dGCLdOM1 = 0.0d0
+      dGCLdOM2 = 0.0d0
+      dGCLdOM12 = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Generalised Born Solvent Polarization
 !c!-------------------------------------------------------------------
 !c! Generalised Born Solvent Polarization
-        ee0 = dexp(-( Rhead_sq ) / (4.0d0 * a12sq))
-        Fgb = sqrt( ( Rhead_sq ) + a12sq * ee0)
-        Egb = -(332.0d0 * Qij * eps_inout_fac) / Fgb
+      ee0 = dexp(-( Rhead_sq ) / (4.0d0 * a12sq))
+      Fgb = sqrt( ( Rhead_sq ) + a12sq * ee0)
+      Egb = -(332.0d0 * Qij * eps_inout_fac) / Fgb
 !c!        Egb = 0.0d0
 !c!      write (*,*) "a1*a2 = ", a12sq
 !c!      write (*,*) "Rhead = ", Rhead
 !c!        Egb = 0.0d0
 !c!      write (*,*) "a1*a2 = ", a12sq
 !c!      write (*,*) "Rhead = ", Rhead
@@ -26489,207 +26341,207 @@
 !c!      write (*,*) "Egb = ", Egb
 !c! Derivative of Egb is Ggb...
 !c! dFGBdR is used by Quad's later...
 !c!      write (*,*) "Egb = ", Egb
 !c! Derivative of Egb is Ggb...
 !c! dFGBdR is used by Quad's later...
-        dGGBdFGB = -(-332.0d0 * Qij * eps_inout_fac) / (Fgb * Fgb)
-        dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )&
-               / ( 2.0d0 * Fgb )
-        dGGBdR = dGGBdFGB * dFGBdR
+      dGGBdFGB = -(-332.0d0 * Qij * eps_inout_fac) / (Fgb * Fgb)
+      dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )&
+             / ( 2.0d0 * Fgb )
+      dGGBdR = dGGBdFGB * dFGBdR
 !c!        dGGBdR = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Fisocav - isotropic cavity creation term
 !c!        dGGBdR = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Fisocav - isotropic cavity creation term
-        pom = Rhead * csig
-        top = al1 * (dsqrt(pom) + al2 * pom - al3)
-        bot = (1.0d0 + al4 * pom**12.0d0)
-        botsq = bot * bot
-        FisoCav = top / bot
-        dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2)
-        dbot = 12.0d0 * al4 * pom ** 11.0d0
-        dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig
+      pom = Rhead * csig
+      top = al1 * (dsqrt(pom) + al2 * pom - al3)
+      bot = (1.0d0 + al4 * pom**12.0d0)
+      botsq = bot * bot
+      FisoCav = top / bot
+      dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2)
+      dbot = 12.0d0 * al4 * pom ** 11.0d0
+      dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig
 !c!        dGCVdR = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Polarization energy
 !c! Epol
 !c!        dGCVdR = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Polarization energy
 !c! Epol
-        MomoFac1 = (1.0d0 - chi1 * sqom2)
-        MomoFac2 = (1.0d0 - chi2 * sqom1)
-        RR1  = ( R1 * R1 ) / MomoFac1
-        RR2  = ( R2 * R2 ) / MomoFac2
-        ee1  = exp(-( RR1 / (4.0d0 * a12sq) ))
-        ee2  = exp(-( RR2 / (4.0d0 * a12sq) ))
-        fgb1 = sqrt( RR1 + a12sq * ee1 )
-        fgb2 = sqrt( RR2 + a12sq * ee2 )
-        epol = 332.0d0 * eps_inout_fac * (&
-        (( alphapol1 / fgb1 )**4.0d0)+((alphapol2/fgb2) ** 4.0d0 ))
+      MomoFac1 = (1.0d0 - chi1 * sqom2)
+      MomoFac2 = (1.0d0 - chi2 * sqom1)
+      RR1  = ( R1 * R1 ) / MomoFac1
+      RR2  = ( R2 * R2 ) / MomoFac2
+      ee1  = exp(-( RR1 / (4.0d0 * a12sq) ))
+      ee2  = exp(-( RR2 / (4.0d0 * a12sq) ))
+      fgb1 = sqrt( RR1 + a12sq * ee1 )
+      fgb2 = sqrt( RR2 + a12sq * ee2 )
+      epol = 332.0d0 * eps_inout_fac * (&
+      (( alphapol1 / fgb1 )**4.0d0)+((alphapol2/fgb2) ** 4.0d0 ))
 !c!        epol = 0.0d0
 !c! derivative of Epol is Gpol...
 !c!        epol = 0.0d0
 !c! derivative of Epol is Gpol...
-        dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0)&
-                  / (fgb1 ** 5.0d0)
-        dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0)&
-                  / (fgb2 ** 5.0d0)
-        dFGBdR1 = ( (R1 / MomoFac1) &
-                * ( 2.0d0 - (0.5d0 * ee1) ) )&
-                / ( 2.0d0 * fgb1 )
-        dFGBdR2 = ( (R2 / MomoFac2) &
-                * ( 2.0d0 - (0.5d0 * ee2) ) ) &
-                / ( 2.0d0 * fgb2 )
-        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
-                 * ( 2.0d0 - 0.5d0 * ee1) ) &
-                 / ( 2.0d0 * fgb1 )
-        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
-                 * ( 2.0d0 - 0.5d0 * ee2) ) &
-                 / ( 2.0d0 * fgb2 )
-        dPOLdR1 = dPOLdFGB1 * dFGBdR1
+      dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0)&
+              / (fgb1 ** 5.0d0)
+      dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0)&
+              / (fgb2 ** 5.0d0)
+      dFGBdR1 = ( (R1 / MomoFac1) &
+            * ( 2.0d0 - (0.5d0 * ee1) ) )&
+            / ( 2.0d0 * fgb1 )
+      dFGBdR2 = ( (R2 / MomoFac2) &
+            * ( 2.0d0 - (0.5d0 * ee2) ) ) &
+            / ( 2.0d0 * fgb2 )
+      dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
+             * ( 2.0d0 - 0.5d0 * ee1) ) &
+             / ( 2.0d0 * fgb1 )
+      dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
+             * ( 2.0d0 - 0.5d0 * ee2) ) &
+             / ( 2.0d0 * fgb2 )
+      dPOLdR1 = dPOLdFGB1 * dFGBdR1
 !c!        dPOLdR1 = 0.0d0
 !c!        dPOLdR1 = 0.0d0
-        dPOLdR2 = dPOLdFGB2 * dFGBdR2
+      dPOLdR2 = dPOLdFGB2 * dFGBdR2
 !c!        dPOLdR2 = 0.0d0
 !c!        dPOLdR2 = 0.0d0
-        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
+      dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!        dPOLdOM1 = 0.0d0
 !c!        dPOLdOM1 = 0.0d0
-        dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
-        pom = (pis / Rhead)**6.0d0
-        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
+      dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
+      pom = (pis / Rhead)**6.0d0
+      Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c!        Elj = 0.0d0
 !c! derivative of Elj is Glj
 !c!        Elj = 0.0d0
 !c! derivative of Elj is Glj
-        dGLJdR = 4.0d0 * eps_head &
-            * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
-            +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+      dGLJdR = 4.0d0 * eps_head &
+          * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
+          +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
 !c!        dGLJdR = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Equad
        IF (Wqd.ne.0.0d0) THEN
 !c!        dGLJdR = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Equad
        IF (Wqd.ne.0.0d0) THEN
-        Beta1 = 5.0d0 + 3.0d0 * (sqom12 - 1.0d0) &
-             - 37.5d0  * ( sqom1 + sqom2 ) &
-             + 157.5d0 * ( sqom1 * sqom2 ) &
-             - 45.0d0  * om1*om2*om12
-        fac = -( Wqd / (2.0d0 * Fgb**5.0d0) )
-        Equad = fac * Beta1
+      Beta1 = 5.0d0 + 3.0d0 * (sqom12 - 1.0d0) &
+           - 37.5d0  * ( sqom1 + sqom2 ) &
+           + 157.5d0 * ( sqom1 * sqom2 ) &
+           - 45.0d0  * om1*om2*om12
+      fac = -( Wqd / (2.0d0 * Fgb**5.0d0) )
+      Equad = fac * Beta1
 !c!        Equad = 0.0d0
 !c! derivative of Equad...
 !c!        Equad = 0.0d0
 !c! derivative of Equad...
-        dQUADdR = ((2.5d0 * Wqd * Beta1) / (Fgb**6.0d0)) * dFGBdR
+      dQUADdR = ((2.5d0 * Wqd * Beta1) / (Fgb**6.0d0)) * dFGBdR
 !c!        dQUADdR = 0.0d0
 !c!        dQUADdR = 0.0d0
-        dQUADdOM1 = fac* (-75.0d0*om1 + 315.0d0*om1*sqom2 - 45.0d0*om2*om12)
+      dQUADdOM1 = fac* (-75.0d0*om1 + 315.0d0*om1*sqom2 - 45.0d0*om2*om12)
 !c!        dQUADdOM1 = 0.0d0
 !c!        dQUADdOM1 = 0.0d0
-        dQUADdOM2 = fac* (-75.0d0*om2 + 315.0d0*sqom1*om2 - 45.0d0*om1*om12)
+      dQUADdOM2 = fac* (-75.0d0*om2 + 315.0d0*sqom1*om2 - 45.0d0*om1*om12)
 !c!        dQUADdOM2 = 0.0d0
 !c!        dQUADdOM2 = 0.0d0
-        dQUADdOM12 = fac * ( 6.0d0*om12 - 45.0d0*om1*om2 )
+      dQUADdOM12 = fac * ( 6.0d0*om12 - 45.0d0*om1*om2 )
        ELSE
        ELSE
-         Beta1 = 0.0d0
-         Equad = 0.0d0
-        END IF
+       Beta1 = 0.0d0
+       Equad = 0.0d0
+      END IF
 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! Angular stuff
 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! Angular stuff
-        eom1 = dPOLdOM1 + dQUADdOM1
-        eom2 = dPOLdOM2 + dQUADdOM2
-        eom12 = dQUADdOM12
+      eom1 = dPOLdOM1 + dQUADdOM1
+      eom2 = dPOLdOM2 + dQUADdOM2
+      eom12 = dQUADdOM12
 !c! now some magical transformations to project gradient into
 !c! three cartesian vectors
 !c! now some magical transformations to project gradient into
 !c! three cartesian vectors
-        DO k = 1, 3
-         dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k))
-         dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
-         tuna(k) = eom1 * dcosom1(k) + eom2 * dcosom2(k)
-        END DO
+      DO k = 1, 3
+       dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k))
+       dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
+       tuna(k) = eom1 * dcosom1(k) + eom2 * dcosom2(k)
+      END DO
 !c! Radial stuff
 !c! Radial stuff
-        DO k = 1, 3
-         erhead(k) = Rhead_distance(k)/Rhead
-         erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
-         erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
-        END DO
-        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
-        erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
-        bat   = scalar( erhead_tail(1,1), dC_norm(1,i+nres) )
-        federmaus = scalar(erhead_tail(1,1),dC_norm(1,j+nres))
-        eagle = scalar( erhead_tail(1,2), dC_norm(1,j+nres) )
-        adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
-        facd1 = d1 * vbld_inv(i+nres)
-        facd2 = d2 * vbld_inv(j+nres)
-        facd3 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
-        facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
-        DO k = 1, 3
-         hawk   = erhead_tail(k,1) + &
-         facd1 * (erhead_tail(k,1) - bat   * dC_norm(k,i+nres))
-         condor = erhead_tail(k,2) + &
-         facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres))
-
-         pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+      DO k = 1, 3
+       erhead(k) = Rhead_distance(k)/Rhead
+       erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
+       erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+      END DO
+      erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+      erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
+      bat   = scalar( erhead_tail(1,1), dC_norm(1,i+nres) )
+      federmaus = scalar(erhead_tail(1,1),dC_norm(1,j+nres))
+      eagle = scalar( erhead_tail(1,2), dC_norm(1,j+nres) )
+      adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
+      facd1 = d1 * vbld_inv(i+nres)
+      facd2 = d2 * vbld_inv(j+nres)
+      facd3 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
+      facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
+      DO k = 1, 3
+       hawk   = erhead_tail(k,1) + &
+       facd1 * (erhead_tail(k,1) - bat   * dC_norm(k,i+nres))
+       condor = erhead_tail(k,2) + &
+       facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres))
+
+       pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
 !c! this acts on hydrophobic center of interaction
 !c! this acts on hydrophobic center of interaction
-         gheadtail(k,1,1) = gheadtail(k,1,1) &
-                         - dGCLdR * pom &
-                         - dGGBdR * pom &
-                         - dGCVdR * pom &
-                         - dPOLdR1 * hawk &
-                         - dPOLdR2 * (erhead_tail(k,2) &
+       gheadtail(k,1,1) = gheadtail(k,1,1) &
+                   - dGCLdR * pom &
+                   - dGGBdR * pom &
+                   - dGCVdR * pom &
+                   - dPOLdR1 * hawk &
+                   - dPOLdR2 * (erhead_tail(k,2) &
       -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))&
       -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))&
-                         - dGLJdR * pom &
-                         - dQUADdR * pom&
-                         - tuna(k) &
-                 + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))&
-                 + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+                   - dGLJdR * pom &
+                   - dQUADdR * pom&
+                   - tuna(k) &
+             + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))&
+             + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
 
 
-         pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+       pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
 !c! this acts on hydrophobic center of interaction
 !c! this acts on hydrophobic center of interaction
-         gheadtail(k,2,1) = gheadtail(k,2,1)  &
-                         + dGCLdR * pom      &
-                         + dGGBdR * pom      &
-                         + dGCVdR * pom      &
-                         + dPOLdR1 * (erhead_tail(k,1) &
+       gheadtail(k,2,1) = gheadtail(k,2,1)  &
+                   + dGCLdR * pom      &
+                   + dGGBdR * pom      &
+                   + dGCVdR * pom      &
+                   + dPOLdR1 * (erhead_tail(k,1) &
       -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres))) &
       -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres))) &
-                         + dPOLdR2 * condor &
-                         + dGLJdR * pom &
-                         + dQUADdR * pom &
-                         + tuna(k) &
-                 + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
-                 + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+                   + dPOLdR2 * condor &
+                   + dGLJdR * pom &
+                   + dQUADdR * pom &
+                   + tuna(k) &
+             + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
+             + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
 
 !c! this acts on Calpha
 
 !c! this acts on Calpha
-         gheadtail(k,3,1) = gheadtail(k,3,1)  &
-                         - dGCLdR * erhead(k)&
-                         - dGGBdR * erhead(k)&
-                         - dGCVdR * erhead(k)&
-                         - dPOLdR1 * erhead_tail(k,1)&
-                         - dPOLdR2 * erhead_tail(k,2)&
-                         - dGLJdR * erhead(k) &
-                         - dQUADdR * erhead(k)&
-                         - tuna(k)
+       gheadtail(k,3,1) = gheadtail(k,3,1)  &
+                   - dGCLdR * erhead(k)&
+                   - dGGBdR * erhead(k)&
+                   - dGCVdR * erhead(k)&
+                   - dPOLdR1 * erhead_tail(k,1)&
+                   - dPOLdR2 * erhead_tail(k,2)&
+                   - dGLJdR * erhead(k) &
+                   - dQUADdR * erhead(k)&
+                   - tuna(k)
 !c! this acts on Calpha
 !c! this acts on Calpha
-         gheadtail(k,4,1) = gheadtail(k,4,1)   &
-                          + dGCLdR * erhead(k) &
-                          + dGGBdR * erhead(k) &
-                          + dGCVdR * erhead(k) &
-                          + dPOLdR1 * erhead_tail(k,1) &
-                          + dPOLdR2 * erhead_tail(k,2) &
-                          + dGLJdR * erhead(k) &
-                          + dQUADdR * erhead(k)&
-                          + tuna(k)
-        END DO
-        ener(istate) = ECL + Egb + Epol + Fisocav + Elj + Equad
-        eheadtail = eheadtail &
-                  + wstate(istate, itypi, itypj) &
-                  * dexp(-betaT * ener(istate))
+       gheadtail(k,4,1) = gheadtail(k,4,1)   &
+                    + dGCLdR * erhead(k) &
+                    + dGGBdR * erhead(k) &
+                    + dGCVdR * erhead(k) &
+                    + dPOLdR1 * erhead_tail(k,1) &
+                    + dPOLdR2 * erhead_tail(k,2) &
+                    + dGLJdR * erhead(k) &
+                    + dQUADdR * erhead(k)&
+                    + tuna(k)
+      END DO
+      ener(istate) = ECL + Egb + Epol + Fisocav + Elj + Equad
+      eheadtail = eheadtail &
+              + wstate(istate, itypi, itypj) &
+              * dexp(-betaT * ener(istate))
 !c! foreach cartesian dimension
 !c! foreach cartesian dimension
-        DO k = 1, 3
+      DO k = 1, 3
 !c! foreach of two gvdwx and gvdwc
 !c! foreach of two gvdwx and gvdwc
-         DO l = 1, 4
-          gheadtail(k,l,2) = gheadtail(k,l,2)  &
-                           + wstate( istate, itypi, itypj ) &
-                           * dexp(-betaT * ener(istate)) &
-                           * gheadtail(k,l,1)
-          gheadtail(k,l,1) = 0.0d0
-         END DO
-        END DO
+       DO l = 1, 4
+        gheadtail(k,l,2) = gheadtail(k,l,2)  &
+                     + wstate( istate, itypi, itypj ) &
+                     * dexp(-betaT * ener(istate)) &
+                     * gheadtail(k,l,1)
+        gheadtail(k,l,1) = 0.0d0
+       END DO
+      END DO
        END DO
 !c! Here ended the gigantic DO istate = 1, 4, which starts
 !c! at the beggining of the subroutine
 
        DO k = 1, 3
        END DO
 !c! Here ended the gigantic DO istate = 1, 4, which starts
 !c! at the beggining of the subroutine
 
        DO k = 1, 3
-        DO l = 1, 4
-         gheadtail(k,l,2) = gheadtail(k,l,2) / eheadtail
-        END DO
-        gvdwx(k,i) = gvdwx(k,i) + gheadtail(k,1,2)
-        gvdwx(k,j) = gvdwx(k,j) + gheadtail(k,2,2)
-        gvdwc(k,i) = gvdwc(k,i) + gheadtail(k,3,2)
-        gvdwc(k,j) = gvdwc(k,j) + gheadtail(k,4,2)
-        DO l = 1, 4
-         gheadtail(k,l,1) = 0.0d0
-         gheadtail(k,l,2) = 0.0d0
-        END DO
+      DO l = 1, 4
+       gheadtail(k,l,2) = gheadtail(k,l,2) / eheadtail
+      END DO
+      gvdwx(k,i) = gvdwx(k,i) + gheadtail(k,1,2)
+      gvdwx(k,j) = gvdwx(k,j) + gheadtail(k,2,2)
+      gvdwc(k,i) = gvdwc(k,i) + gheadtail(k,3,2)
+      gvdwc(k,j) = gvdwc(k,j) + gheadtail(k,4,2)
+      DO l = 1, 4
+       gheadtail(k,l,1) = 0.0d0
+       gheadtail(k,l,2) = 0.0d0
+      END DO
        END DO
        eheadtail = (-dlog(eheadtail)) / betaT
        dPOLdOM1 = 0.0d0
        END DO
        eheadtail = (-dlog(eheadtail)) / betaT
        dPOLdOM1 = 0.0d0
@@ -26710,7 +26562,7 @@
        R1 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances
        R1 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances
-        R1=R1+(ctail(k,2)-chead(k,1))**2
+      R1=R1+(ctail(k,2)-chead(k,1))**2
        END DO
 !c! Pitagoras
        R1 = dsqrt(R1)
        END DO
 !c! Pitagoras
        R1 = dsqrt(R1)
@@ -26728,19 +26580,19 @@
        fgb1 = sqrt( RR1 + a12sq * ee1)
        epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0)
        dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0) &
        fgb1 = sqrt( RR1 + a12sq * ee1)
        epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0)
        dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0) &
-               / (fgb1 ** 5.0d0)
+             / (fgb1 ** 5.0d0)
        dFGBdR1 = ( (R1 / MomoFac1) &
        dFGBdR1 = ( (R1 / MomoFac1) &
-              * ( 2.0d0 - (0.5d0 * ee1) ) ) &
-              / ( 2.0d0 * fgb1 )
+            * ( 2.0d0 - (0.5d0 * ee1) ) ) &
+            / ( 2.0d0 * fgb1 )
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
-                * (2.0d0 - 0.5d0 * ee1) ) &
-                / (2.0d0 * fgb1)
+            * (2.0d0 - 0.5d0 * ee1) ) &
+            / (2.0d0 * fgb1)
        dPOLdR1 = dPOLdFGB1 * dFGBdR1
 !c!       dPOLdR1 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
        DO k = 1, 3
        dPOLdR1 = dPOLdFGB1 * dFGBdR1
 !c!       dPOLdR1 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
        DO k = 1, 3
-        erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
+      erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
        END DO
        bat = scalar( erhead_tail(1,1), dC_norm(1,i+nres) )
        federmaus = scalar(erhead_tail(1,1),dC_norm(1,j+nres))
        END DO
        bat = scalar( erhead_tail(1,1), dC_norm(1,i+nres) )
        federmaus = scalar(erhead_tail(1,1),dC_norm(1,j+nres))
@@ -26748,17 +26600,17 @@
        facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
 
        DO k = 1, 3
        facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
 
        DO k = 1, 3
-        hawk = (erhead_tail(k,1) + &
-        facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
+      hawk = (erhead_tail(k,1) + &
+      facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
 
 
-        gvdwx(k,i) = gvdwx(k,i) &
-                   - dPOLdR1 * hawk
-        gvdwx(k,j) = gvdwx(k,j) &
-                   + dPOLdR1 * (erhead_tail(k,1) &
+      gvdwx(k,i) = gvdwx(k,i) &
+               - dPOLdR1 * hawk
+      gvdwx(k,j) = gvdwx(k,j) &
+               + dPOLdR1 * (erhead_tail(k,1) &
        -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres)))
 
        -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres)))
 
-        gvdwc(k,i) = gvdwc(k,i)  - dPOLdR1 * erhead_tail(k,1)
-        gvdwc(k,j) = gvdwc(k,j)  + dPOLdR1 * erhead_tail(k,1)
+      gvdwc(k,i) = gvdwc(k,i)  - dPOLdR1 * erhead_tail(k,1)
+      gvdwc(k,j) = gvdwc(k,j)  + dPOLdR1 * erhead_tail(k,1)
 
        END DO
        RETURN
 
        END DO
        RETURN
@@ -26772,7 +26624,7 @@
        R2 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances
        R2 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances
-        R2=R2+(chead(k,2)-ctail(k,1))**2
+      R2=R2+(chead(k,2)-ctail(k,1))**2
        END DO
 !c! Pitagoras
        R2 = dsqrt(R2)
        END DO
 !c! Pitagoras
        R2 = dsqrt(R2)
@@ -26789,13 +26641,13 @@
        fgb2 = sqrt(RR2  + a12sq * ee2)
        epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 )
        dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) &
        fgb2 = sqrt(RR2  + a12sq * ee2)
        epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 )
        dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) &
-                / (fgb2 ** 5.0d0)
+            / (fgb2 ** 5.0d0)
        dFGBdR2 = ( (R2 / MomoFac2)  &
        dFGBdR2 = ( (R2 / MomoFac2)  &
-              * ( 2.0d0 - (0.5d0 * ee2) ) ) &
-              / (2.0d0 * fgb2)
+            * ( 2.0d0 - (0.5d0 * ee2) ) ) &
+            / (2.0d0 * fgb2)
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
-                * (2.0d0 - 0.5d0 * ee2) ) &
-                / (2.0d0 * fgb2)
+            * (2.0d0 - 0.5d0 * ee2) ) &
+            / (2.0d0 * fgb2)
        dPOLdR2 = dPOLdFGB2 * dFGBdR2
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
        dPOLdR2 = dPOLdFGB2 * dFGBdR2
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
@@ -26805,26 +26657,26 @@
 !c! Return the results
 !c! (See comments in Eqq)
        DO k = 1, 3
 !c! Return the results
 !c! (See comments in Eqq)
        DO k = 1, 3
-        erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+      erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
        END DO
        eagle = scalar( erhead_tail(1,2), dC_norm(1,j+nres) )
        adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
        facd2 = d2 * vbld_inv(j+nres)
        facd3 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
        DO k = 1, 3
        END DO
        eagle = scalar( erhead_tail(1,2), dC_norm(1,j+nres) )
        adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
        facd2 = d2 * vbld_inv(j+nres)
        facd3 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
        DO k = 1, 3
-        condor = (erhead_tail(k,2) &
+      condor = (erhead_tail(k,2) &
        + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres)))
 
        + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres)))
 
-        gvdwx(k,i) = gvdwx(k,i) &
-                   - dPOLdR2 * (erhead_tail(k,2) &
+      gvdwx(k,i) = gvdwx(k,i) &
+               - dPOLdR2 * (erhead_tail(k,2) &
        -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))
        -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))
-        gvdwx(k,j) = gvdwx(k,j)   &
-                   + dPOLdR2 * condor
+      gvdwx(k,j) = gvdwx(k,j)   &
+               + dPOLdR2 * condor
 
 
-        gvdwc(k,i) = gvdwc(k,i) &
-                   - dPOLdR2 * erhead_tail(k,2)
-        gvdwc(k,j) = gvdwc(k,j) &
-                   + dPOLdR2 * erhead_tail(k,2)
+      gvdwc(k,i) = gvdwc(k,i) &
+               - dPOLdR2 * erhead_tail(k,2)
+      gvdwc(k,j) = gvdwc(k,j) &
+               + dPOLdR2 * erhead_tail(k,2)
 
        END DO
       RETURN
 
        END DO
       RETURN
@@ -26834,12 +26686,12 @@
       use calc_data
       use comm_momo
        double precision facd3, adler,epol
       use calc_data
       use comm_momo
        double precision facd3, adler,epol
-       alphapol2 = alphapolcat(itypj,itypi)
+       alphapol2 = alphapolcat(itypi,itypj)
 !c! R2 - distance between head of jth side chain and tail of ith sidechain
        R2 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances
 !c! R2 - distance between head of jth side chain and tail of ith sidechain
        R2 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances
-        R2=R2+(chead(k,2)-ctail(k,1))**2
+      R2=R2+(chead(k,2)-ctail(k,1))**2
        END DO
 !c! Pitagoras
        R2 = dsqrt(R2)
        END DO
 !c! Pitagoras
        R2 = dsqrt(R2)
@@ -26856,13 +26708,13 @@
        fgb2 = sqrt(RR2  + a12sq * ee2)
        epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 )
        dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) &
        fgb2 = sqrt(RR2  + a12sq * ee2)
        epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 )
        dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) &
-                / (fgb2 ** 5.0d0)
+            / (fgb2 ** 5.0d0)
        dFGBdR2 = ( (R2 / MomoFac2)  &
        dFGBdR2 = ( (R2 / MomoFac2)  &
-              * ( 2.0d0 - (0.5d0 * ee2) ) ) &
-              / (2.0d0 * fgb2)
+            * ( 2.0d0 - (0.5d0 * ee2) ) ) &
+            / (2.0d0 * fgb2)
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
-                * (2.0d0 - 0.5d0 * ee2) ) &
-                / (2.0d0 * fgb2)
+            * (2.0d0 - 0.5d0 * ee2) ) &
+            / (2.0d0 * fgb2)
        dPOLdR2 = dPOLdFGB2 * dFGBdR2
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
        dPOLdR2 = dPOLdFGB2 * dFGBdR2
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
@@ -26873,26 +26725,26 @@
 !c! Return the results
 !c! (See comments in Eqq)
        DO k = 1, 3
 !c! Return the results
 !c! (See comments in Eqq)
        DO k = 1, 3
-        erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+      erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
        END DO
        eagle = scalar( erhead_tail(1,2), dC_norm(1,j) )
        adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
        facd2 = d2 * vbld_inv(j+nres)
        facd3 = dtailcat(1,itypi,itypj) * vbld_inv(i+nres)
        DO k = 1, 3
        END DO
        eagle = scalar( erhead_tail(1,2), dC_norm(1,j) )
        adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
        facd2 = d2 * vbld_inv(j+nres)
        facd3 = dtailcat(1,itypi,itypj) * vbld_inv(i+nres)
        DO k = 1, 3
-        condor = (erhead_tail(k,2) &
+      condor = (erhead_tail(k,2) &
        + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j)))
 
        + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j)))
 
-        gvdwx(k,i) = gvdwx(k,i) &
-                   - dPOLdR2 * (erhead_tail(k,2) &
+      gradpepcatx(k,i) = gradpepcatx(k,i) &
+               - dPOLdR2 * (erhead_tail(k,2) &
        -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))
        -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))
-        gvdwx(k,j) = gvdwx(k,j)   &
-                   + dPOLdR2 * condor
+!        gradpepcatx(k,j) = gradpepcatx(k,j)   &
+!                   + dPOLdR2 * condor
 
 
-        gvdwc(k,i) = gvdwc(k,i) &
-                   - dPOLdR2 * erhead_tail(k,2)
-        gvdwc(k,j) = gvdwc(k,j) &
-                   + dPOLdR2 * erhead_tail(k,2)
+      gradpepcat(k,i) = gradpepcat(k,i) &
+               - dPOLdR2 * erhead_tail(k,2)
+      gradpepcat(k,j) = gradpepcat(k,j) &
+               + dPOLdR2 * erhead_tail(k,2)
 
        END DO
       RETURN
 
        END DO
       RETURN
@@ -26912,7 +26764,7 @@
        R1 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances
        R1 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances
-        R1=R1+(ctail(k,2)-chead(k,1))**2
+      R1=R1+(ctail(k,2)-chead(k,1))**2
        END DO
 !c! Pitagoras
        R1 = dsqrt(R1)
        END DO
 !c! Pitagoras
        R1 = dsqrt(R1)
@@ -26927,9 +26779,9 @@
        sparrow  = w1 * Qi * om1
        hawk     = w2 * Qi * Qi * (1.0d0 - sqom2)
        Ecl = sparrow / Rhead**2.0d0 &
        sparrow  = w1 * Qi * om1
        hawk     = w2 * Qi * Qi * (1.0d0 - sqom2)
        Ecl = sparrow / Rhead**2.0d0 &
-           - hawk    / Rhead**4.0d0
+         - hawk    / Rhead**4.0d0
        dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
        dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
-                 + 4.0d0 * hawk    / Rhead**5.0d0
+             + 4.0d0 * hawk    / Rhead**5.0d0
 !c! dF/dom1
        dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0)
 !c! dF/dom2
 !c! dF/dom1
        dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0)
 !c! dF/dom2
@@ -26946,13 +26798,13 @@
 !c!------------------------------------------------------------------
 !c! derivative of Epol is Gpol...
        dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0) &
 !c!------------------------------------------------------------------
 !c! derivative of Epol is Gpol...
        dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0) &
-               / (fgb1 ** 5.0d0)
+             / (fgb1 ** 5.0d0)
        dFGBdR1 = ( (R1 / MomoFac1)  &
        dFGBdR1 = ( (R1 / MomoFac1)  &
-             * ( 2.0d0 - (0.5d0 * ee1) ) ) &
-             / ( 2.0d0 * fgb1 )
+           * ( 2.0d0 - (0.5d0 * ee1) ) ) &
+           / ( 2.0d0 * fgb1 )
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
-               * (2.0d0 - 0.5d0 * ee1) ) &
-               / (2.0d0 * fgb1)
+             * (2.0d0 - 0.5d0 * ee1) ) &
+             / (2.0d0 * fgb1)
        dPOLdR1 = dPOLdFGB1 * dFGBdR1
 !c!       dPOLdR1 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdR1 = dPOLdFGB1 * dFGBdR1
 !c!       dPOLdR1 = 0.0d0
        dPOLdOM1 = 0.0d0
@@ -26964,11 +26816,11 @@
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head &
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head &
-          * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
-          +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+        * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
+        +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
        DO k = 1, 3
        DO k = 1, 3
-        erhead(k) = Rhead_distance(k)/Rhead
-        erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
+      erhead(k) = Rhead_distance(k)/Rhead
+      erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
        END DO
 
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
        END DO
 
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
@@ -26980,32 +26832,32 @@
        facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
 
        DO k = 1, 3
        facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
 
        DO k = 1, 3
-        hawk = (erhead_tail(k,1) +  &
-        facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
-
-        pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
-        gvdwx(k,i) = gvdwx(k,i)  &
-                   - dGCLdR * pom&
-                   - dPOLdR1 * hawk &
-                   - dGLJdR * pom  
-
-        pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
-        gvdwx(k,j) = gvdwx(k,j)    &
-                   + dGCLdR * pom  &
-                   + dPOLdR1 * (erhead_tail(k,1) &
+      hawk = (erhead_tail(k,1) +  &
+      facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
+
+      pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+      gvdwx(k,i) = gvdwx(k,i)  &
+               - dGCLdR * pom&
+               - dPOLdR1 * hawk &
+               - dGLJdR * pom  
+
+      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+      gvdwx(k,j) = gvdwx(k,j)    &
+               + dGCLdR * pom  &
+               + dPOLdR1 * (erhead_tail(k,1) &
        -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres))) &
        -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres))) &
-                   + dGLJdR * pom
+               + dGLJdR * pom
 
 
 
 
-        gvdwc(k,i) = gvdwc(k,i)          &
-                   - dGCLdR * erhead(k)  &
-                   - dPOLdR1 * erhead_tail(k,1) &
-                   - dGLJdR * erhead(k)
+      gvdwc(k,i) = gvdwc(k,i)          &
+               - dGCLdR * erhead(k)  &
+               - dPOLdR1 * erhead_tail(k,1) &
+               - dGLJdR * erhead(k)
 
 
-        gvdwc(k,j) = gvdwc(k,j)          &
-                   + dGCLdR * erhead(k)  &
-                   + dPOLdR1 * erhead_tail(k,1) &
-                   + dGLJdR * erhead(k)
+      gvdwc(k,j) = gvdwc(k,j)          &
+               + dGCLdR * erhead(k)  &
+               + dPOLdR1 * erhead_tail(k,1) &
+               + dGLJdR * erhead(k)
 
        END DO
        RETURN
 
        END DO
        RETURN
@@ -27026,7 +26878,7 @@
        R2 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances
        R2 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances
-        R2=R2+(chead(k,2)-ctail(k,1))**2
+      R2=R2+(chead(k,2)-ctail(k,1))**2
        END DO
 !c! Pitagoras
        R2 = dsqrt(R2)
        END DO
 !c! Pitagoras
        R2 = dsqrt(R2)
@@ -27039,19 +26891,19 @@
 
 !c!-------------------------------------------------------------------
 !c! ecl
 
 !c!-------------------------------------------------------------------
 !c! ecl
-       sparrow  = w1 * Qi * om1
-       hawk     = w2 * Qi * Qi * (1.0d0 - sqom2)
+       sparrow  = w1 * Qj * om1
+       hawk     = w2 * Qj * Qj * (1.0d0 - sqom2)
        ECL = sparrow / Rhead**2.0d0 &
        ECL = sparrow / Rhead**2.0d0 &
-           - hawk    / Rhead**4.0d0
+         - hawk    / Rhead**4.0d0
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part
        dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part
        dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
-                 + 4.0d0 * hawk    / Rhead**5.0d0
+             + 4.0d0 * hawk    / Rhead**5.0d0
 !c! dF/dom1
 !c! dF/dom1
-       dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0)
+       dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
 !c! dF/dom2
 !c! dF/dom2
-       dGCLdOM2 = (2.0d0 * w2 * Qi * Qi * om2) / (Rhead ** 4.0d0)
+       dGCLdOM2 = (2.0d0 * w2 * Qj * Qj * om2) / (Rhead ** 4.0d0)
 !c--------------------------------------------------------------------
 !c Polarization energy
 !c Epol
 !c--------------------------------------------------------------------
 !c Polarization energy
 !c Epol
@@ -27061,13 +26913,13 @@
        fgb2 = sqrt(RR2  + a12sq * ee2)
        epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 )
        dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) &
        fgb2 = sqrt(RR2  + a12sq * ee2)
        epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 )
        dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) &
-               / (fgb2 ** 5.0d0)
+             / (fgb2 ** 5.0d0)
        dFGBdR2 = ( (R2 / MomoFac2)  &
        dFGBdR2 = ( (R2 / MomoFac2)  &
-               * ( 2.0d0 - (0.5d0 * ee2) ) ) &
-               / (2.0d0 * fgb2)
+             * ( 2.0d0 - (0.5d0 * ee2) ) ) &
+             / (2.0d0 * fgb2)
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
-                * (2.0d0 - 0.5d0 * ee2) ) &
-                / (2.0d0 * fgb2)
+            * (2.0d0 - 0.5d0 * ee2) ) &
+            / (2.0d0 * fgb2)
        dPOLdR2 = dPOLdFGB2 * dFGBdR2
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
        dPOLdR2 = dPOLdFGB2 * dFGBdR2
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
@@ -27079,14 +26931,14 @@
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head &
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head &
-           * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
-           +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+         * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
+         +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! (see comments in Eqq)
        DO k = 1, 3
 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! (see comments in Eqq)
        DO k = 1, 3
-        erhead(k) = Rhead_distance(k)/Rhead
-        erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+      erhead(k) = Rhead_distance(k)/Rhead
+      erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
        END DO
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
        erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
        END DO
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
        erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
@@ -27096,43 +26948,162 @@
        facd2 = d2 * vbld_inv(j+nres)
        facd3 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
        DO k = 1, 3
        facd2 = d2 * vbld_inv(j+nres)
        facd3 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
        DO k = 1, 3
-        condor = (erhead_tail(k,2) &
+      condor = (erhead_tail(k,2) &
        + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres)))
 
        + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres)))
 
-        pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
-        gvdwx(k,i) = gvdwx(k,i) &
-                  - dGCLdR * pom &
-                  - dPOLdR2 * (erhead_tail(k,2) &
+      pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+      gvdwx(k,i) = gvdwx(k,i) &
+              - dGCLdR * pom &
+              - dPOLdR2 * (erhead_tail(k,2) &
+       -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres))) &
+              - dGLJdR * pom
+
+      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+      gvdwx(k,j) = gvdwx(k,j) &
+              + dGCLdR * pom &
+              + dPOLdR2 * condor &
+              + dGLJdR * pom
+
+
+      gvdwc(k,i) = gvdwc(k,i) &
+              - dGCLdR * erhead(k) &
+              - dPOLdR2 * erhead_tail(k,2) &
+              - dGLJdR * erhead(k)
+
+      gvdwc(k,j) = gvdwc(k,j) &
+              + dGCLdR * erhead(k) &
+              + dPOLdR2 * erhead_tail(k,2) &
+              + dGLJdR * erhead(k)
+
+       END DO
+       RETURN
+      END SUBROUTINE edq
+
+      SUBROUTINE edq_cat(Ecl,Elj,Epol)
+      use comm_momo
+      use calc_data
+
+      double precision  facd3, adler,ecl,elj,epol
+       alphapol2 = alphapolcat(itypi,itypj)
+       w1        = wqdipcat(1,itypi,itypj)
+       w2        = wqdipcat(2,itypi,itypj)
+       pis       = sig0headcat(itypi,itypj)
+       eps_head  = epsheadcat(itypi,itypj)
+!c!-------------------------------------------------------------------
+!c! R2 - distance between head of jth side chain and tail of ith sidechain
+       R2 = 0.0d0
+       DO k = 1, 3
+!c! Calculate head-to-tail distances
+      R2=R2+(chead(k,2)-ctail(k,1))**2
+       END DO
+!c! Pitagoras
+       R2 = dsqrt(R2)
+
+!c!      R1     = dsqrt((Rtail**2)+((dtail(1,itypi,itypj)
+!c!     &        +dhead(1,1,itypi,itypj))**2))
+!c!      R2     = dsqrt((Rtail**2)+((dtail(2,itypi,itypj)
+!c!     &        +dhead(2,1,itypi,itypj))**2))
+
+
+!c!-------------------------------------------------------------------
+!c! ecl
+!       write(iout,*) "KURWA2",Rhead
+       sparrow  = w1 * Qj * om1
+       hawk     = w2 * Qj * Qj * (1.0d0 - sqom2)
+       ECL = sparrow / Rhead**2.0d0 &
+         - hawk    / Rhead**4.0d0
+!c!-------------------------------------------------------------------
+!c! derivative of ecl is Gcl
+!c! dF/dr part
+       dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
+             + 4.0d0 * hawk    / Rhead**5.0d0
+!c! dF/dom1
+       dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
+!c! dF/dom2
+       dGCLdOM2 = (2.0d0 * w2 * Qj * Qj * om2) / (Rhead ** 4.0d0)
+!c--------------------------------------------------------------------
+!c--------------------------------------------------------------------
+!c Polarization energy
+!c Epol
+       MomoFac2 = (1.0d0 - chi2 * sqom1)
+       RR2  = R2 * R2 / MomoFac2
+       ee2  = exp(-(RR2 / (4.0d0 * a12sq)))
+       fgb2 = sqrt(RR2  + a12sq * ee2)
+       epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 )
+       dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) &
+             / (fgb2 ** 5.0d0)
+       dFGBdR2 = ( (R2 / MomoFac2)  &
+             * ( 2.0d0 - (0.5d0 * ee2) ) ) &
+             / (2.0d0 * fgb2)
+       dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
+            * (2.0d0 - 0.5d0 * ee2) ) &
+            / (2.0d0 * fgb2)
+       dPOLdR2 = dPOLdFGB2 * dFGBdR2
+!c!       dPOLdR2 = 0.0d0
+       dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
+!c!       dPOLdOM1 = 0.0d0
+       dPOLdOM2 = 0.0d0
+!c!-------------------------------------------------------------------
+!c! Elj
+       pom = (pis / Rhead)**6.0d0
+       Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
+!c! derivative of Elj is Glj
+       dGLJdR = 4.0d0 * eps_head &
+         * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
+         +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+!c!-------------------------------------------------------------------
+
+!c! Return the results
+!c! (see comments in Eqq)
+       DO k = 1, 3
+      erhead(k) = Rhead_distance(k)/Rhead
+      erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+       END DO
+       erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+       erdxj = scalar( erhead(1), dC_norm(1,j) )
+       eagle = scalar( erhead_tail(1,2), dC_norm(1,j) )
+       adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
+       facd1 = d1 * vbld_inv(i+nres)
+       facd2 = d2 * vbld_inv(j)
+       facd3 = dtailcat(1,itypi,itypj) * vbld_inv(i+nres)
+       DO k = 1, 3
+      condor = (erhead_tail(k,2) &
+       + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j)))
+
+      pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+      gradpepcatx(k,i) = gradpepcatx(k,i) &
+              - dGCLdR * pom &
+              - dPOLdR2 * (erhead_tail(k,2) &
        -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres))) &
        -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres))) &
-                  - dGLJdR * pom
+              - dGLJdR * pom
 
 
-        pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
-        gvdwx(k,j) = gvdwx(k,j) &
-                  + dGCLdR * pom &
-                  + dPOLdR2 * condor &
-                  + dGLJdR * pom
+      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j))
+!        gradpepcatx(k,j) = gradpepcatx(k,j) &
+!                  + dGCLdR * pom &
+!                  + dPOLdR2 * condor &
+!                  + dGLJdR * pom
 
 
 
 
-        gvdwc(k,i) = gvdwc(k,i) &
-                  - dGCLdR * erhead(k) &
-                  - dPOLdR2 * erhead_tail(k,2) &
-                  - dGLJdR * erhead(k)
+      gradpepcat(k,i) = gradpepcat(k,i) &
+              - dGCLdR * erhead(k) &
+              - dPOLdR2 * erhead_tail(k,2) &
+              - dGLJdR * erhead(k)
 
 
-        gvdwc(k,j) = gvdwc(k,j) &
-                  + dGCLdR * erhead(k) &
-                  + dPOLdR2 * erhead_tail(k,2) &
-                  + dGLJdR * erhead(k)
+      gradpepcat(k,j) = gradpepcat(k,j) &
+              + dGCLdR * erhead(k) &
+              + dPOLdR2 * erhead_tail(k,2) &
+              + dGLJdR * erhead(k)
 
        END DO
        RETURN
 
        END DO
        RETURN
-      END SUBROUTINE edq
+      END SUBROUTINE edq_cat
 
 
-      SUBROUTINE edq_cat(Ecl,Elj,Epol)
+      SUBROUTINE edq_cat_pep(Ecl,Elj,Epol)
       use comm_momo
       use calc_data
 
       double precision  facd3, adler,ecl,elj,epol
       use comm_momo
       use calc_data
 
       double precision  facd3, adler,ecl,elj,epol
-       alphapol2 = alphapolcat(itypj,itypi)
+       alphapol2 = alphapolcat(itypi,itypj)
        w1        = wqdipcat(1,itypi,itypj)
        w2        = wqdipcat(2,itypi,itypj)
        pis       = sig0headcat(itypi,itypj)
        w1        = wqdipcat(1,itypi,itypj)
        w2        = wqdipcat(2,itypi,itypj)
        pis       = sig0headcat(itypi,itypj)
@@ -27142,7 +27113,7 @@
        R2 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances
        R2 = 0.0d0
        DO k = 1, 3
 !c! Calculate head-to-tail distances
-        R2=R2+(chead(k,2)-ctail(k,1))**2
+      R2=R2+(chead(k,2)-ctail(k,1))**2
        END DO
 !c! Pitagoras
        R2 = dsqrt(R2)
        END DO
 !c! Pitagoras
        R2 = dsqrt(R2)
@@ -27155,19 +27126,21 @@
 
 !c!-------------------------------------------------------------------
 !c! ecl
 
 !c!-------------------------------------------------------------------
 !c! ecl
-       sparrow  = w1 * Qi * om1
-       hawk     = w2 * Qi * Qi * (1.0d0 - sqom2)
+       sparrow  = w1 * Qj * om1
+       hawk     = w2 * Qj * Qj * (1.0d0 - sqom2)
+!       print *,"CO2", itypi,itypj
+!       print *,"CO?!.", w1,w2,Qj,om1
        ECL = sparrow / Rhead**2.0d0 &
        ECL = sparrow / Rhead**2.0d0 &
-           - hawk    / Rhead**4.0d0
+         - hawk    / Rhead**4.0d0
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part
        dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part
        dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
-                 + 4.0d0 * hawk    / Rhead**5.0d0
+             + 4.0d0 * hawk    / Rhead**5.0d0
 !c! dF/dom1
 !c! dF/dom1
-       dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0)
+       dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
 !c! dF/dom2
 !c! dF/dom2
-       dGCLdOM2 = (2.0d0 * w2 * Qi * Qi * om2) / (Rhead ** 4.0d0)
+       dGCLdOM2 = (2.0d0 * w2 * Qj * Qj * om2) / (Rhead ** 4.0d0)
 !c--------------------------------------------------------------------
 !c--------------------------------------------------------------------
 !c Polarization energy
 !c--------------------------------------------------------------------
 !c--------------------------------------------------------------------
 !c Polarization energy
@@ -27178,13 +27151,13 @@
        fgb2 = sqrt(RR2  + a12sq * ee2)
        epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 )
        dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) &
        fgb2 = sqrt(RR2  + a12sq * ee2)
        epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 )
        dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) &
-               / (fgb2 ** 5.0d0)
+             / (fgb2 ** 5.0d0)
        dFGBdR2 = ( (R2 / MomoFac2)  &
        dFGBdR2 = ( (R2 / MomoFac2)  &
-               * ( 2.0d0 - (0.5d0 * ee2) ) ) &
-               / (2.0d0 * fgb2)
+             * ( 2.0d0 - (0.5d0 * ee2) ) ) &
+             / (2.0d0 * fgb2)
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
-                * (2.0d0 - 0.5d0 * ee2) ) &
-                / (2.0d0 * fgb2)
+            * (2.0d0 - 0.5d0 * ee2) ) &
+            / (2.0d0 * fgb2)
        dPOLdR2 = dPOLdFGB2 * dFGBdR2
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
        dPOLdR2 = dPOLdFGB2 * dFGBdR2
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
@@ -27196,55 +27169,59 @@
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head &
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head &
-           * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
-           +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+         * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
+         +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
 !c!-------------------------------------------------------------------
 
 !c! Return the results
 !c! (see comments in Eqq)
        DO k = 1, 3
 !c!-------------------------------------------------------------------
 
 !c! Return the results
 !c! (see comments in Eqq)
        DO k = 1, 3
-        erhead(k) = Rhead_distance(k)/Rhead
-        erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+      erhead(k) = Rhead_distance(k)/Rhead
+      erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
        END DO
        END DO
-       erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+       erdxi = scalar( erhead(1), dC_norm(1,i) )
        erdxj = scalar( erhead(1), dC_norm(1,j) )
        eagle = scalar( erhead_tail(1,2), dC_norm(1,j) )
        erdxj = scalar( erhead(1), dC_norm(1,j) )
        eagle = scalar( erhead_tail(1,2), dC_norm(1,j) )
-       adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
-       facd1 = d1 * vbld_inv(i+nres)
+       adler = scalar( erhead_tail(1,2), dC_norm(1,i) )
+       facd1 = d1 * vbld_inv(i+1)/2.0
        facd2 = d2 * vbld_inv(j)
        facd2 = d2 * vbld_inv(j)
-       facd3 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
+       facd3 = dtailcat(1,itypi,itypj) * vbld_inv(i+1)/2.0
        DO k = 1, 3
        DO k = 1, 3
-        condor = (erhead_tail(k,2) &
+      condor = (erhead_tail(k,2) &
        + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j)))
 
        + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j)))
 
-        pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
-        gvdwx(k,i) = gvdwx(k,i) &
-                  - dGCLdR * pom &
-                  - dPOLdR2 * (erhead_tail(k,2) &
-       -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres))) &
-                  - dGLJdR * pom
+      pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i))
+!        gradpepcatx(k,i) = gradpepcatx(k,i) &
+!                  - dGCLdR * pom &
+!                  - dPOLdR2 * (erhead_tail(k,2) &
+!       -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres))) &
+!                  - dGLJdR * pom
+
+      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j))
+!        gradpepcatx(k,j) = gradpepcatx(k,j) &
+!                  + dGCLdR * pom &
+!                  + dPOLdR2 * condor &
+!                  + dGLJdR * pom
 
 
-        pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j))
-        gvdwx(k,j) = gvdwx(k,j) &
-                  + dGCLdR * pom &
-                  + dPOLdR2 * condor &
-                  + dGLJdR * pom
 
 
+      gradpepcat(k,i) = gradpepcat(k,i) +0.5d0*( &
+              - dGCLdR * erhead(k) &
+              - dPOLdR2 * erhead_tail(k,2) &
+              - dGLJdR * erhead(k))
+      gradpepcat(k,i+1) = gradpepcat(k,i+1) +0.5d0*( &
+              - dGCLdR * erhead(k) &
+              - dPOLdR2 * erhead_tail(k,2) &
+              - dGLJdR * erhead(k))
 
 
-        gvdwc(k,i) = gvdwc(k,i) &
-                  - dGCLdR * erhead(k) &
-                  - dPOLdR2 * erhead_tail(k,2) &
-                  - dGLJdR * erhead(k)
 
 
-        gvdwc(k,j) = gvdwc(k,j) &
-                  + dGCLdR * erhead(k) &
-                  + dPOLdR2 * erhead_tail(k,2) &
-                  + dGLJdR * erhead(k)
+      gradpepcat(k,j) = gradpepcat(k,j) &
+              + dGCLdR * erhead(k) &
+              + dPOLdR2 * erhead_tail(k,2) &
+              + dGLJdR * erhead(k)
 
        END DO
        RETURN
 
        END DO
        RETURN
-      END SUBROUTINE edq_cat
-
+      END SUBROUTINE edq_cat_pep
 
       SUBROUTINE edd(ECL)
 !       IMPLICIT NONE
 
       SUBROUTINE edd(ECL)
 !       IMPLICIT NONE
@@ -27260,7 +27237,7 @@
        fac = (om12 - 3.0d0 * om1 * om2)
        c1 = (w1 / (Rhead**3.0d0)) * fac
        c2 = (w2 / Rhead ** 6.0d0) &
        fac = (om12 - 3.0d0 * om1 * om2)
        c1 = (w1 / (Rhead**3.0d0)) * fac
        c2 = (w2 / Rhead ** 6.0d0) &
-          * (4.0d0 + fac * fac -3.0d0 * (sqom1 + sqom2))
+        * (4.0d0 + fac * fac -3.0d0 * (sqom1 + sqom2))
        ECL = c1 - c2
 !c!       write (*,*) "w1 = ", w1
 !c!       write (*,*) "w2 = ", w2
        ECL = c1 - c2
 !c!       write (*,*) "w1 = ", w1
 !c!       write (*,*) "w2 = ", w2
@@ -27279,17 +27256,17 @@
 !c! dECL/dr
        c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
        c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) &
 !c! dECL/dr
        c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
        c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) &
-          * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2))
+        * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2))
        dGCLdR = c1 - c2
 !c! dECL/dom1
        c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
        dGCLdR = c1 - c2
 !c! dECL/dom1
        c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
-          * ( om2 * om12 - 3.0d0 * om1 * sqom2 + om1 )
+        * ( om2 * om12 - 3.0d0 * om1 * sqom2 + om1 )
        dGCLdOM1 = c1 - c2
 !c! dECL/dom2
        c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
        dGCLdOM1 = c1 - c2
 !c! dECL/dom2
        c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
-          * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 )
+        * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 )
        dGCLdOM2 = c1 - c2
 !c! dECL/dom12
        c1 = w1 / (Rhead ** 3.0d0)
        dGCLdOM2 = c1 - c2
 !c! dECL/dom12
        c1 = w1 / (Rhead ** 3.0d0)
@@ -27299,7 +27276,7 @@
 !c! Return the results
 !c! (see comments in Eqq)
        DO k= 1, 3
 !c! Return the results
 !c! (see comments in Eqq)
        DO k= 1, 3
-        erhead(k) = Rhead_distance(k)/Rhead
+      erhead(k) = Rhead_distance(k)/Rhead
        END DO
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
        erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
        END DO
        erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
        erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
@@ -27307,13 +27284,13 @@
        facd2 = d2 * vbld_inv(j+nres)
        DO k = 1, 3
 
        facd2 = d2 * vbld_inv(j+nres)
        DO k = 1, 3
 
-        pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
-        gvdwx(k,i) = gvdwx(k,i)    - dGCLdR * pom
-        pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
-        gvdwx(k,j) = gvdwx(k,j)    + dGCLdR * pom
+      pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+      gvdwx(k,i) = gvdwx(k,i)    - dGCLdR * pom
+      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+      gvdwx(k,j) = gvdwx(k,j)    + dGCLdR * pom
 
 
-        gvdwc(k,i) = gvdwc(k,i)    - dGCLdR * erhead(k)
-        gvdwc(k,j) = gvdwc(k,j)    + dGCLdR * erhead(k)
+      gvdwc(k,i) = gvdwc(k,i)    - dGCLdR * erhead(k)
+      gvdwc(k,j) = gvdwc(k,j)    + dGCLdR * erhead(k)
        END DO
        RETURN
       END SUBROUTINE edd
        END DO
        RETURN
       END SUBROUTINE edd
@@ -27394,8 +27371,8 @@
 !c! tail location and distance calculations
        Rtail = 0.0d0
        DO k = 1, 3
 !c! tail location and distance calculations
        Rtail = 0.0d0
        DO k = 1, 3
-        ctail(k,1)=c(k,i+nres)-dtail(1,itypi,itypj)*dc_norm(k,nres+i)
-        ctail(k,2)=c(k,j+nres)-dtail(2,itypi,itypj)*dc_norm(k,nres+j)
+      ctail(k,1)=c(k,i+nres)-dtail(1,itypi,itypj)*dc_norm(k,nres+i)
+      ctail(k,2)=c(k,j+nres)-dtail(2,itypi,itypj)*dc_norm(k,nres+j)
        END DO
 !c! tail distances will be themselves usefull elswhere
 !c1 (in Gcav, for example)
        END DO
 !c! tail distances will be themselves usefull elswhere
 !c1 (in Gcav, for example)
@@ -27403,9 +27380,9 @@
        Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 )
        Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 )
        Rtail = dsqrt(  &
        Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 )
        Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 )
        Rtail = dsqrt(  &
-          (Rtail_distance(1)*Rtail_distance(1))  &
-        + (Rtail_distance(2)*Rtail_distance(2))  &
-        + (Rtail_distance(3)*Rtail_distance(3)))
+        (Rtail_distance(1)*Rtail_distance(1))  &
+      + (Rtail_distance(2)*Rtail_distance(2))  &
+      + (Rtail_distance(3)*Rtail_distance(3)))
 !c!-------------------------------------------------------------------
 !c! Calculate location and distance between polar heads
 !c! distance between heads
 !c!-------------------------------------------------------------------
 !c! Calculate location and distance between polar heads
 !c! distance between heads
@@ -27417,18 +27394,18 @@
 !c! location of polar head is computed by taking hydrophobic centre
 !c! and moving by a d1 * dc_norm vector
 !c! see unres publications for very informative images
 !c! location of polar head is computed by taking hydrophobic centre
 !c! and moving by a d1 * dc_norm vector
 !c! see unres publications for very informative images
-        chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
-        chead(k,2) = c(k, j+nres) + d2 * dc_norm(k, j+nres)
+      chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
+      chead(k,2) = c(k, j+nres) + d2 * dc_norm(k, j+nres)
 !c! distance 
 !c!        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
 !c!        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
 !c! distance 
 !c!        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
 !c!        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
-        Rhead_distance(k) = chead(k,2) - chead(k,1)
+      Rhead_distance(k) = chead(k,2) - chead(k,1)
        END DO
 !c! pitagoras (root of sum of squares)
        Rhead = dsqrt(   &
        END DO
 !c! pitagoras (root of sum of squares)
        Rhead = dsqrt(   &
-          (Rhead_distance(1)*Rhead_distance(1)) &
-        + (Rhead_distance(2)*Rhead_distance(2)) &
-        + (Rhead_distance(3)*Rhead_distance(3)))
+        (Rhead_distance(1)*Rhead_distance(1)) &
+      + (Rhead_distance(2)*Rhead_distance(2)) &
+      + (Rhead_distance(3)*Rhead_distance(3)))
 !c!-------------------------------------------------------------------
 !c! zero everything that should be zero'ed
        Egb = 0.0d0
 !c!-------------------------------------------------------------------
 !c! zero everything that should be zero'ed
        Egb = 0.0d0
@@ -27452,7 +27429,7 @@
        real(kind=8) :: eheadtail,Egb,Ecl,Elj,Equad,Epol,Rb
        eps_out=80.0d0
        itypi = itype(i,1)
        real(kind=8) :: eheadtail,Egb,Ecl,Elj,Equad,Epol,Rb
        eps_out=80.0d0
        itypi = itype(i,1)
-       itypj = itype(j,1)
+       itypj = itype(j,5)
 !c! 1/(Gas Constant * Thermostate temperature) = BetaT
 !c! ENABLE THIS LINE WHEN USING CHECKGRAD!!!
 !c!       t_bath = 300
 !c! 1/(Gas Constant * Thermostate temperature) = BetaT
 !c! ENABLE THIS LINE WHEN USING CHECKGRAD!!!
 !c!       t_bath = 300
@@ -27461,55 +27438,38 @@
        BetaT = 1.0d0 / (298.0d0 * Rb)
 !c! Gay-berne var's
        sig0ij = sigmacat( itypi,itypj )
        BetaT = 1.0d0 / (298.0d0 * Rb)
 !c! Gay-berne var's
        sig0ij = sigmacat( itypi,itypj )
-       chi1   = chicat( itypi, itypj )
-!       chi2   = chi( itypj, itypi )
+       chi1   = chi1cat( itypi, itypj )
        chi2   = 0.0d0
        chi2   = 0.0d0
-!       chi12  = chi1 * chi2
        chi12  = 0.0d0
        chi12  = 0.0d0
-       chip1  = chippcat( itypi, itypj )
-!       chip2  = chipp( itypj, itypi )
+       chip1  = chipp1cat( itypi, itypj )
        chip2  = 0.0d0
        chip2  = 0.0d0
-!       chip12 = chip1 * chip2
        chip12 = 0.0d0
        chip12 = 0.0d0
-!       chi1=0.0
-!       chi2=0.0
-!       chi12=0.0
-!       chip1=0.0
-!       chip2=0.0
-!       chip12=0.0
 !c! not used by momo potential, but needed by sc_angular which is shared
 !c! by all energy_potential subroutines
        alf1   = 0.0d0
        alf2   = 0.0d0
        alf12  = 0.0d0
 !c! not used by momo potential, but needed by sc_angular which is shared
 !c! by all energy_potential subroutines
        alf1   = 0.0d0
        alf2   = 0.0d0
        alf12  = 0.0d0
-!c! location, location, location
-!       xj  = c( 1, nres+j ) - xi
-!       yj  = c( 2, nres+j ) - yi
-!       zj  = c( 3, nres+j ) - zi
-       dxj = dc_norm( 1, nres+j )
-       dyj = dc_norm( 2, nres+j )
-       dzj = dc_norm( 3, nres+j )
+       dxj = 0.0d0 !dc_norm( 1, nres+j )
+       dyj = 0.0d0 !dc_norm( 2, nres+j )
+       dzj = 0.0d0 !dc_norm( 3, nres+j )
 !c! distance from center of chain(?) to polar/charged head
        d1 = dheadcat(1, 1, itypi, itypj)
        d2 = dheadcat(2, 1, itypi, itypj)
 !c! ai*aj from Fgb
 !c! distance from center of chain(?) to polar/charged head
        d1 = dheadcat(1, 1, itypi, itypj)
        d2 = dheadcat(2, 1, itypi, itypj)
 !c! ai*aj from Fgb
-       a12sq = rborncat(itypi,itypj) * rborncat(itypj,itypi)
+       a12sq = rborn1cat(itypi,itypj) * rborn2cat(itypi,itypj)
 !c!       a12sq = a12sq * a12sq
 !c! charge of amino acid itypi is...
 !c!       a12sq = a12sq * a12sq
 !c! charge of amino acid itypi is...
-       Qi  = ichargecat(itypi)
+       Qi  = icharge(itypi)
        Qj  = ichargecat(itypj)
        Qij = Qi * Qj
 !c! chis1,2,12
        Qj  = ichargecat(itypj)
        Qij = Qi * Qj
 !c! chis1,2,12
-       chis1 = chiscat(itypi,itypj)
-!       chis2 = chis(itypj,itypi)
+       chis1 = chis1cat(itypi,itypj)
        chis2 = 0.0d0
        chis2 = 0.0d0
-!       chis12 = chis1 * chis2
        chis12 = 0.0d0
        sig1 = sigmap1cat(itypi,itypj)
        sig2 = sigmap2cat(itypi,itypj)
 !c! alpha factors from Fcav/Gcav
        b1cav = alphasurcat(1,itypi,itypj)
        chis12 = 0.0d0
        sig1 = sigmap1cat(itypi,itypj)
        sig2 = sigmap2cat(itypi,itypj)
 !c! alpha factors from Fcav/Gcav
        b1cav = alphasurcat(1,itypi,itypj)
-!       b1cav=0.0
        b2cav = alphasurcat(2,itypi,itypj)
        b3cav = alphasurcat(3,itypi,itypj)
        b4cav = alphasurcat(4,itypi,itypj)
        b2cav = alphasurcat(2,itypi,itypj)
        b3cav = alphasurcat(3,itypi,itypj)
        b4cav = alphasurcat(4,itypi,itypj)
@@ -27521,8 +27481,8 @@
 !c! tail location and distance calculations
        Rtail = 0.0d0
        DO k = 1, 3
 !c! tail location and distance calculations
        Rtail = 0.0d0
        DO k = 1, 3
-        ctail(k,1)=c(k,i+nres)-dtailcat(1,itypi,itypj)*dc_norm(k,nres+i)
-        ctail(k,2)=c(k,j+nres)-dtailcat(2,itypi,itypj)*dc_norm(k,nres+j)
+      ctail(k,1)=c(k,i+nres)-dtailcat(1,itypi,itypj)*dc_norm(k,nres+i)
+      ctail(k,2)=c(k,j)!-dtailcat(2,itypi,itypj)*dc_norm(k,nres+j)
        END DO
 !c! tail distances will be themselves usefull elswhere
 !c1 (in Gcav, for example)
        END DO
 !c! tail distances will be themselves usefull elswhere
 !c1 (in Gcav, for example)
@@ -27530,9 +27490,9 @@
        Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 )
        Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 )
        Rtail = dsqrt(  &
        Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 )
        Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 )
        Rtail = dsqrt(  &
-          (Rtail_distance(1)*Rtail_distance(1))  &
-        + (Rtail_distance(2)*Rtail_distance(2))  &
-        + (Rtail_distance(3)*Rtail_distance(3)))
+        (Rtail_distance(1)*Rtail_distance(1))  &
+      + (Rtail_distance(2)*Rtail_distance(2))  &
+      + (Rtail_distance(3)*Rtail_distance(3)))
 !c!-------------------------------------------------------------------
 !c! Calculate location and distance between polar heads
 !c! distance between heads
 !c!-------------------------------------------------------------------
 !c! Calculate location and distance between polar heads
 !c! distance between heads
@@ -27544,18 +27504,18 @@
 !c! location of polar head is computed by taking hydrophobic centre
 !c! and moving by a d1 * dc_norm vector
 !c! see unres publications for very informative images
 !c! location of polar head is computed by taking hydrophobic centre
 !c! and moving by a d1 * dc_norm vector
 !c! see unres publications for very informative images
-        chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
-        chead(k,2) = c(k, j+nres) + d2 * dc_norm(k, j+nres)
+      chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
+      chead(k,2) = c(k, j) 
 !c! distance 
 !c!        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
 !c!        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
 !c! distance 
 !c!        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
 !c!        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
-        Rhead_distance(k) = chead(k,2) - chead(k,1)
+      Rhead_distance(k) = chead(k,2) - chead(k,1)
        END DO
 !c! pitagoras (root of sum of squares)
        Rhead = dsqrt(   &
        END DO
 !c! pitagoras (root of sum of squares)
        Rhead = dsqrt(   &
-          (Rhead_distance(1)*Rhead_distance(1)) &
-        + (Rhead_distance(2)*Rhead_distance(2)) &
-        + (Rhead_distance(3)*Rhead_distance(3)))
+        (Rhead_distance(1)*Rhead_distance(1)) &
+      + (Rhead_distance(2)*Rhead_distance(2)) &
+      + (Rhead_distance(3)*Rhead_distance(3)))
 !c!-------------------------------------------------------------------
 !c! zero everything that should be zero'ed
        Egb = 0.0d0
 !c!-------------------------------------------------------------------
 !c! zero everything that should be zero'ed
        Egb = 0.0d0
@@ -27572,6 +27532,114 @@
        RETURN
       END SUBROUTINE elgrad_init_cat
 
        RETURN
       END SUBROUTINE elgrad_init_cat
 
+      SUBROUTINE elgrad_init_cat_pep(eheadtail,Egb,Ecl,Elj,Equad,Epol)
+      use comm_momo
+      use calc_data
+       real(kind=8) :: eheadtail,Egb,Ecl,Elj,Equad,Epol,Rb
+       eps_out=80.0d0
+       itypi = 10
+       itypj = itype(j,5)
+!c! 1/(Gas Constant * Thermostate temperature) = BetaT
+!c! ENABLE THIS LINE WHEN USING CHECKGRAD!!!
+!c!       t_bath = 300
+!c!       BetaT = 1.0d0 / (t_bath * Rb)i
+       Rb=0.001986d0
+       BetaT = 1.0d0 / (298.0d0 * Rb)
+!c! Gay-berne var's
+       sig0ij = sigmacat( itypi,itypj )
+       chi1   = chi1cat( itypi, itypj )
+       chi2   = 0.0d0
+       chi12  = 0.0d0
+       chip1  = chipp1cat( itypi, itypj )
+       chip2  = 0.0d0
+       chip12 = 0.0d0
+!c! not used by momo potential, but needed by sc_angular which is shared
+!c! by all energy_potential subroutines
+       alf1   = 0.0d0
+       alf2   = 0.0d0
+       alf12  = 0.0d0
+       dxj = 0.0d0 !dc_norm( 1, nres+j )
+       dyj = 0.0d0 !dc_norm( 2, nres+j )
+       dzj = 0.0d0 !dc_norm( 3, nres+j )
+!c! distance from center of chain(?) to polar/charged head
+       d1 = dheadcat(1, 1, itypi, itypj)
+       d2 = dheadcat(2, 1, itypi, itypj)
+!c! ai*aj from Fgb
+       a12sq = rborn1cat(itypi,itypj) * rborn2cat(itypi,itypj)
+!c!       a12sq = a12sq * a12sq
+!c! charge of amino acid itypi is...
+       Qi  = 0
+       Qj  = ichargecat(itypj)
+!       Qij = Qi * Qj
+!c! chis1,2,12
+       chis1 = chis1cat(itypi,itypj)
+       chis2 = 0.0d0
+       chis12 = 0.0d0
+       sig1 = sigmap1cat(itypi,itypj)
+       sig2 = sigmap2cat(itypi,itypj)
+!c! alpha factors from Fcav/Gcav
+       b1cav = alphasurcat(1,itypi,itypj)
+       b2cav = alphasurcat(2,itypi,itypj)
+       b3cav = alphasurcat(3,itypi,itypj)
+       b4cav = alphasurcat(4,itypi,itypj)
+       wqd = wquadcat(itypi, itypj)
+!c! used by Fgb
+       eps_in = epsintabcat(itypi,itypj)
+       eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out))
+!c!-------------------------------------------------------------------
+!c! tail location and distance calculations
+       Rtail = 0.0d0
+       DO k = 1, 3
+      ctail(k,1)=(c(k,i)+c(k,i+1))/2.0-dtailcat(1,itypi,itypj)*dc_norm(k,i)
+      ctail(k,2)=c(k,j)!-dtailcat(2,itypi,itypj)*dc_norm(k,nres+j)
+       END DO
+!c! tail distances will be themselves usefull elswhere
+!c1 (in Gcav, for example)
+       Rtail_distance(1) = ctail( 1, 2 ) - ctail( 1,1 )
+       Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 )
+       Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 )
+       Rtail = dsqrt(  &
+        (Rtail_distance(1)*Rtail_distance(1))  &
+      + (Rtail_distance(2)*Rtail_distance(2))  &
+      + (Rtail_distance(3)*Rtail_distance(3)))
+!c!-------------------------------------------------------------------
+!c! Calculate location and distance between polar heads
+!c! distance between heads
+!c! for each one of our three dimensional space...
+       d1 = dheadcat(1, 1, itypi, itypj)
+       d2 = dheadcat(2, 1, itypi, itypj)
+
+       DO k = 1,3
+!c! location of polar head is computed by taking hydrophobic centre
+!c! and moving by a d1 * dc_norm vector
+!c! see unres publications for very informative images
+      chead(k,1) = (c(k, i)+c(k,i+1))/2.0 + d1 * dc_norm(k, i)
+      chead(k,2) = c(k, j) 
+!c! distance 
+!c!        Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
+!c!        Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
+      Rhead_distance(k) = chead(k,2) - chead(k,1)
+       END DO
+!c! pitagoras (root of sum of squares)
+       Rhead = dsqrt(   &
+        (Rhead_distance(1)*Rhead_distance(1)) &
+      + (Rhead_distance(2)*Rhead_distance(2)) &
+      + (Rhead_distance(3)*Rhead_distance(3)))
+!c!-------------------------------------------------------------------
+!c! zero everything that should be zero'ed
+       Egb = 0.0d0
+       ECL = 0.0d0
+       Elj = 0.0d0
+       Equad = 0.0d0
+       Epol = 0.0d0
+       eheadtail = 0.0d0
+       dGCLdOM1 = 0.0d0
+       dGCLdOM2 = 0.0d0
+       dGCLdOM12 = 0.0d0
+       dPOLdOM1 = 0.0d0
+       dPOLdOM2 = 0.0d0
+       RETURN
+      END SUBROUTINE elgrad_init_cat_pep
 
       double precision function tschebyshev(m,n,x,y)
       implicit none
 
       double precision function tschebyshev(m,n,x,y)
       implicit none
@@ -27583,11 +27651,11 @@
       yy(0)=1.0d0
       yy(1)=y
       do i=2,n
       yy(0)=1.0d0
       yy(1)=y
       do i=2,n
-        yy(i)=2*yy(1)*yy(i-1)-yy(i-2)
+      yy(i)=2*yy(1)*yy(i-1)-yy(i-2)
       enddo
       aux=0.0d0
       do i=m,n
       enddo
       aux=0.0d0
       do i=m,n
-        aux=aux+x(i)*yy(i)
+      aux=aux+x(i)*yy(i)
       enddo
       tschebyshev=aux
       return
       enddo
       tschebyshev=aux
       return
@@ -27603,19 +27671,430 @@
       yy(0)=1.0d0
       yy(1)=2.0d0*y
       do i=2,n
       yy(0)=1.0d0
       yy(1)=2.0d0*y
       do i=2,n
-        yy(i)=2*y*yy(i-1)-yy(i-2)
+      yy(i)=2*y*yy(i-1)-yy(i-2)
       enddo
       aux=0.0d0
       do i=m,n
       enddo
       aux=0.0d0
       do i=m,n
-        aux=aux+x(i+1)*yy(i)*(i+1)
+      aux=aux+x(i+1)*yy(i)*(i+1)
 !C        print *, x(i+1),yy(i),i
       enddo
       gradtschebyshev=aux
       return
       end function gradtschebyshev
 
 !C        print *, x(i+1),yy(i),i
       enddo
       gradtschebyshev=aux
       return
       end function gradtschebyshev
 
+      subroutine make_SCSC_inter_list
+      include 'mpif.h'
+      real*8 :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp
+      real*8 :: dist_init, dist_temp,r_buff_list
+      integer:: contlisti(250*nres),contlistj(250*nres)
+!      integer :: newcontlisti(200*nres),newcontlistj(200*nres) 
+      integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_sc,g_ilist_sc
+      integer displ(0:nprocs),i_ilist_sc(0:nprocs),ierr
+!            print *,"START make_SC"
+        r_buff_list=5.0
+          ilist_sc=0
+          do i=iatsc_s,iatsc_e
+           itypi=iabs(itype(i,1))
+           if (itypi.eq.ntyp1) cycle
+           xi=c(1,nres+i)
+           yi=c(2,nres+i)
+           zi=c(3,nres+i)
+          call to_box(xi,yi,zi)
+           do iint=1,nint_gr(i)
+!           print *,"is it wrong", iint,i
+            do j=istart(i,iint),iend(i,iint)
+             itypj=iabs(itype(j,1))
+             if (energy_dec) write(iout,*) "LISTA ZAKRES",istart(i,iint),iend(i,iint),iatsc_s,iatsc_e
+             if (itypj.eq.ntyp1) cycle
+             xj=c(1,nres+j)
+             yj=c(2,nres+j)
+             zj=c(3,nres+j)
+             call to_box(xj,yj,zj)
+!          call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+!          faclipij2=(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0
+          xj=boxshift(xj-xi,boxxsize)
+          yj=boxshift(yj-yi,boxysize)
+          zj=boxshift(zj-zi,boxzsize)
+          dist_init=xj**2+yj**2+zj**2
+!             dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+! r_buff_list is a read value for a buffer 
+             if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then
+! Here the list is created
+             ilist_sc=ilist_sc+1
+! this can be substituted by cantor and anti-cantor
+             contlisti(ilist_sc)=i
+             contlistj(ilist_sc)=j
+
+             endif
+           enddo
+           enddo
+           enddo
+!         call MPI_Reduce(ilist_sc,g_ilist_sc,1,&
+!          MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
+!        call MPI_Gather(newnss,1,MPI_INTEGER,&
+!                        i_newnss,1,MPI_INTEGER,king,FG_COMM,IERR)
+#ifdef DEBUG
+      write (iout,*) "before MPIREDUCE",ilist_sc
+      do i=1,ilist_sc
+      write (iout,*) i,contlisti(i),contlistj(i)
+      enddo
+#endif
+      if (nfgtasks.gt.1)then
+
+      call MPI_Reduce(ilist_sc,g_ilist_sc,1,&
+        MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
+!        write(iout,*) "before bcast",g_ilist_sc
+      call MPI_Gather(ilist_sc,1,MPI_INTEGER,&
+                  i_ilist_sc,1,MPI_INTEGER,king,FG_COMM,IERR)
+      displ(0)=0
+      do i=1,nfgtasks-1,1
+        displ(i)=i_ilist_sc(i-1)+displ(i-1)
+      enddo
+!        write(iout,*) "before gather",displ(0),displ(1)        
+      call MPI_Gatherv(contlisti,ilist_sc,MPI_INTEGER,&
+                   newcontlisti,i_ilist_sc,displ,MPI_INTEGER,&
+                   king,FG_COMM,IERR)
+      call MPI_Gatherv(contlistj,ilist_sc,MPI_INTEGER,&
+                   newcontlistj,i_ilist_sc,displ,MPI_INTEGER,&
+                   king,FG_COMM,IERR)
+      call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM,IERR)
+!        write(iout,*) "before bcast",g_ilist_sc
+!        call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
+      call MPI_Bcast(newcontlisti,g_ilist_sc,MPI_INT,king,FG_COMM,IERR)
+      call MPI_Bcast(newcontlistj,g_ilist_sc,MPI_INT,king,FG_COMM,IERR)
+
+!        call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
+
+      else
+      g_ilist_sc=ilist_sc
+
+      do i=1,ilist_sc
+      newcontlisti(i)=contlisti(i)
+      newcontlistj(i)=contlistj(i)
+      enddo
+      endif
+      
+#ifdef DEBUG
+      write (iout,*) "after MPIREDUCE",g_ilist_sc
+      do i=1,g_ilist_sc
+      write (iout,*) i,newcontlisti(i),newcontlistj(i)
+      enddo
+#endif
+      call int_bounds(g_ilist_sc,g_listscsc_start,g_listscsc_end)
+      return
+      end subroutine make_SCSC_inter_list
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+      subroutine make_SCp_inter_list
+      use MD_data,  only: itime_mat
+
+      include 'mpif.h'
+      real*8 :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp
+      real*8 :: dist_init, dist_temp,r_buff_list
+      integer:: contlistscpi(350*nres),contlistscpj(350*nres)
+!      integer :: newcontlistscpi(200*nres),newcontlistscpj(200*nres)
+      integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_scp,g_ilist_scp
+      integer displ(0:nprocs),i_ilist_scp(0:nprocs),ierr
+!            print *,"START make_SC"
+      r_buff_list=5.0
+          ilist_scp=0
+      do i=iatscp_s,iatscp_e
+      if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
+      xi=0.5D0*(c(1,i)+c(1,i+1))
+      yi=0.5D0*(c(2,i)+c(2,i+1))
+      zi=0.5D0*(c(3,i)+c(3,i+1))
+        call to_box(xi,yi,zi)
+      do iint=1,nscp_gr(i)
+
+      do j=iscpstart(i,iint),iscpend(i,iint)
+        itypj=iabs(itype(j,1))
+        if (itypj.eq.ntyp1) cycle
+! Uncomment following three lines for SC-p interactions
+!         xj=c(1,nres+j)-xi
+!         yj=c(2,nres+j)-yi
+!         zj=c(3,nres+j)-zi
+! Uncomment following three lines for Ca-p interactions
+!          xj=c(1,j)-xi
+!          yj=c(2,j)-yi
+!          zj=c(3,j)-zi
+        xj=c(1,j)
+        yj=c(2,j)
+        zj=c(3,j)
+        call to_box(xj,yj,zj)
+      xj=boxshift(xj-xi,boxxsize)
+      yj=boxshift(yj-yi,boxysize)
+      zj=boxshift(zj-zi,boxzsize)        
+      dist_init=xj**2+yj**2+zj**2
+#ifdef DEBUG
+            ! r_buff_list is a read value for a buffer 
+             if ((sqrt(dist_init).le.(r_cut_ele)).and.(ifirstrun.eq.0)) then
+! Here the list is created
+             ilist_scp_first=ilist_scp_first+1
+! this can be substituted by cantor and anti-cantor
+             contlistscpi_f(ilist_scp_first)=i
+             contlistscpj_f(ilist_scp_first)=j
+            endif
+#endif
+! r_buff_list is a read value for a buffer 
+             if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then
+! Here the list is created
+             ilist_scp=ilist_scp+1
+! this can be substituted by cantor and anti-cantor
+             contlistscpi(ilist_scp)=i
+             contlistscpj(ilist_scp)=j
+            endif
+           enddo
+           enddo
+           enddo
+#ifdef DEBUG
+      write (iout,*) "before MPIREDUCE",ilist_scp
+      do i=1,ilist_scp
+      write (iout,*) i,contlistscpi(i),contlistscpj(i)
+      enddo
+#endif
+      if (nfgtasks.gt.1)then
+
+      call MPI_Reduce(ilist_scp,g_ilist_scp,1,&
+        MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
+!        write(iout,*) "before bcast",g_ilist_sc
+      call MPI_Gather(ilist_scp,1,MPI_INTEGER,&
+                  i_ilist_scp,1,MPI_INTEGER,king,FG_COMM,IERR)
+      displ(0)=0
+      do i=1,nfgtasks-1,1
+        displ(i)=i_ilist_scp(i-1)+displ(i-1)
+      enddo
+!        write(iout,*) "before gather",displ(0),displ(1)
+      call MPI_Gatherv(contlistscpi,ilist_scp,MPI_INTEGER,&
+                   newcontlistscpi,i_ilist_scp,displ,MPI_INTEGER,&
+                   king,FG_COMM,IERR)
+      call MPI_Gatherv(contlistscpj,ilist_scp,MPI_INTEGER,&
+                   newcontlistscpj,i_ilist_scp,displ,MPI_INTEGER,&
+                   king,FG_COMM,IERR)
+      call MPI_Bcast(g_ilist_scp,1,MPI_INT,king,FG_COMM,IERR)
+!        write(iout,*) "before bcast",g_ilist_sc
+!        call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
+      call MPI_Bcast(newcontlistscpi,g_ilist_scp,MPI_INT,king,FG_COMM,IERR)
+      call MPI_Bcast(newcontlistscpj,g_ilist_scp,MPI_INT,king,FG_COMM,IERR)
+
+!        call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
+
+      else
+      g_ilist_scp=ilist_scp
+
+      do i=1,ilist_scp
+      newcontlistscpi(i)=contlistscpi(i)
+      newcontlistscpj(i)=contlistscpj(i)
+      enddo
+      endif
+
+#ifdef DEBUG
+      write (iout,*) "after MPIREDUCE",g_ilist_scp
+      do i=1,g_ilist_scp
+      write (iout,*) i,newcontlistscpi(i),newcontlistscpj(i)
+      enddo
+
+!      if (ifirstrun.eq.0) ifirstrun=1
+!      do i=1,ilist_scp_first
+!       do j=1,g_ilist_scp
+!        if ((newcontlistscpi(j).eq.contlistscpi_f(i)).and.&
+!         (newcontlistscpj(j).eq.contlistscpj_f(i))) go to 126
+!        enddo
+!       print *,itime_mat,"ERROR matrix needs updating"
+!       print *,contlistscpi_f(i),contlistscpj_f(i)
+!  126  continue
+!      enddo
+#endif
+      call int_bounds(g_ilist_scp,g_listscp_start,g_listscp_end)
+
+      return
+      end subroutine make_SCp_inter_list
+
+!-----------------------------------------------------------------------------
+!-----------------------------------------------------------------------------
+
+
+      subroutine make_pp_inter_list
+      include 'mpif.h'
+      real*8 :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp
+      real*8 :: xmedj,ymedj,zmedj,sslipi,ssgradlipi,faclipij2,sslipj,ssgradlipj
+      real*8 :: dist_init, dist_temp,r_buff_list,dxi,dyi,dzi,xmedi,ymedi,zmedi
+      real*8 :: dx_normi,dy_normi,dz_normi,dxj,dyj,dzj,dx_normj,dy_normj,dz_normj
+      integer:: contlistppi(250*nres),contlistppj(250*nres)
+!      integer :: newcontlistppi(200*nres),newcontlistppj(200*nres)
+      integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_pp,g_ilist_pp
+      integer displ(0:nprocs),i_ilist_pp(0:nprocs),ierr
+!            write(iout,*),"START make_pp",iatel_s,iatel_e,r_cut_ele+r_buff_list
+            ilist_pp=0
+      r_buff_list=5.0
+      do i=iatel_s,iatel_e
+        if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
+        dxi=dc(1,i)
+        dyi=dc(2,i)
+        dzi=dc(3,i)
+        dx_normi=dc_norm(1,i)
+        dy_normi=dc_norm(2,i)
+        dz_normi=dc_norm(3,i)
+        xmedi=c(1,i)+0.5d0*dxi
+        ymedi=c(2,i)+0.5d0*dyi
+        zmedi=c(3,i)+0.5d0*dzi
+
+        call to_box(xmedi,ymedi,zmedi)
+        call lipid_layer(xmedi,ymedi,zmedi,sslipi,ssgradlipi)
+!          write (iout,*) i,j,itype(i,1),itype(j,1)
+!          if (itype(j,1).eq.ntyp1.or. itype(j+1,1).eq.ntyp1) cycle
+ 
+! 1,j)
+             do j=ielstart(i),ielend(i)
+!          write (iout,*) i,j,itype(i,1),itype(j,1)
+          if (itype(j,1).eq.ntyp1.or. itype(j+1,1).eq.ntyp1) cycle
+          dxj=dc(1,j)
+          dyj=dc(2,j)
+          dzj=dc(3,j)
+          dx_normj=dc_norm(1,j)
+          dy_normj=dc_norm(2,j)
+          dz_normj=dc_norm(3,j)
+!          xj=c(1,j)+0.5D0*dxj-xmedi
+!          yj=c(2,j)+0.5D0*dyj-ymedi
+!          zj=c(3,j)+0.5D0*dzj-zmedi
+          xj=c(1,j)+0.5D0*dxj
+          yj=c(2,j)+0.5D0*dyj
+          zj=c(3,j)+0.5D0*dzj
+          call to_box(xj,yj,zj)
+!          call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+!          faclipij2=(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0
+          xj=boxshift(xj-xmedi,boxxsize)
+          yj=boxshift(yj-ymedi,boxysize)
+          zj=boxshift(zj-zmedi,boxzsize)
+          dist_init=xj**2+yj**2+zj**2
+      if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then
+! Here the list is created
+                 ilist_pp=ilist_pp+1
+! this can be substituted by cantor and anti-cantor
+                 contlistppi(ilist_pp)=i
+                 contlistppj(ilist_pp)=j
+              endif
+!             enddo
+             enddo
+             enddo
+#ifdef DEBUG
+      write (iout,*) "before MPIREDUCE",ilist_pp
+      do i=1,ilist_pp
+      write (iout,*) i,contlistppi(i),contlistppj(i)
+      enddo
+#endif
+      if (nfgtasks.gt.1)then
+
+        call MPI_Reduce(ilist_pp,g_ilist_pp,1,&
+          MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
+!        write(iout,*) "before bcast",g_ilist_sc
+        call MPI_Gather(ilist_pp,1,MPI_INTEGER,&
+                        i_ilist_pp,1,MPI_INTEGER,king,FG_COMM,IERR)
+        displ(0)=0
+        do i=1,nfgtasks-1,1
+          displ(i)=i_ilist_pp(i-1)+displ(i-1)
+        enddo
+!        write(iout,*) "before gather",displ(0),displ(1)
+        call MPI_Gatherv(contlistppi,ilist_pp,MPI_INTEGER,&
+                         newcontlistppi,i_ilist_pp,displ,MPI_INTEGER,&
+                         king,FG_COMM,IERR)
+        call MPI_Gatherv(contlistppj,ilist_pp,MPI_INTEGER,&
+                         newcontlistppj,i_ilist_pp,displ,MPI_INTEGER,&
+                         king,FG_COMM,IERR)
+        call MPI_Bcast(g_ilist_pp,1,MPI_INT,king,FG_COMM,IERR)
+!        write(iout,*) "before bcast",g_ilist_sc
+!        call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
+        call MPI_Bcast(newcontlistppi,g_ilist_pp,MPI_INT,king,FG_COMM,IERR)
+        call MPI_Bcast(newcontlistppj,g_ilist_pp,MPI_INT,king,FG_COMM,IERR)
+
+!        call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
 
 
+        else
+        g_ilist_pp=ilist_pp
 
 
+        do i=1,ilist_pp
+        newcontlistppi(i)=contlistppi(i)
+        newcontlistppj(i)=contlistppj(i)
+        enddo
+        endif
+        call int_bounds(g_ilist_pp,g_listpp_start,g_listpp_end)
+#ifdef DEBUG
+      write (iout,*) "after MPIREDUCE",g_ilist_pp
+      do i=1,g_ilist_pp
+      write (iout,*) i,newcontlistppi(i),newcontlistppj(i)
+      enddo
+#endif
+      return
+      end subroutine make_pp_inter_list
 
 
+!-----------------------------------------------------------------------------
+      double precision function boxshift(x,boxsize)
+      implicit none
+      double precision x,boxsize
+      double precision xtemp
+      xtemp=dmod(x,boxsize)
+      if (dabs(xtemp-boxsize).lt.dabs(xtemp)) then
+        boxshift=xtemp-boxsize
+      else if (dabs(xtemp+boxsize).lt.dabs(xtemp)) then
+        boxshift=xtemp+boxsize
+      else
+        boxshift=xtemp
+      endif
+      return
+      end function boxshift
+!-----------------------------------------------------------------------------
+      subroutine to_box(xi,yi,zi)
+      implicit none
+!      include 'DIMENSIONS'
+!      include 'COMMON.CHAIN'
+      double precision xi,yi,zi
+      xi=dmod(xi,boxxsize)
+      if (xi.lt.0.0d0) xi=xi+boxxsize
+      yi=dmod(yi,boxysize)
+      if (yi.lt.0.0d0) yi=yi+boxysize
+      zi=dmod(zi,boxzsize)
+      if (zi.lt.0.0d0) zi=zi+boxzsize
+      return
+      end subroutine to_box
+!--------------------------------------------------------------------------
+      subroutine lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+      implicit none
+!      include 'DIMENSIONS'
+!      include 'COMMON.IOUNITS'
+!      include 'COMMON.CHAIN'
+      double precision xi,yi,zi,sslipi,ssgradlipi
+      double precision fracinbuf
+!      double precision sscalelip,sscagradlip
+#ifdef DEBUG
+      write (iout,*) "bordlipbot",bordlipbot," bordliptop",bordliptop
+      write (iout,*) "buflipbot",buflipbot," lipbufthick",lipbufthick
+      write (iout,*) "xi yi zi",xi,yi,zi
+#endif
+      if ((zi.gt.bordlipbot).and.(zi.lt.bordliptop)) then
+! the energy transfer exist
+        if (zi.lt.buflipbot) then
+! what fraction I am in
+          fracinbuf=1.0d0-((zi-bordlipbot)/lipbufthick)
+! lipbufthick is thickenes of lipid buffore
+          sslipi=sscalelip(fracinbuf)
+          ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+        elseif (zi.gt.bufliptop) then
+          fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
+          sslipi=sscalelip(fracinbuf)
+          ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+        else
+          sslipi=1.0d0
+          ssgradlipi=0.0
+        endif
+      else
+        sslipi=0.0d0
+        ssgradlipi=0.0
+      endif
+#ifdef DEBUG
+      write (iout,*) "sslipi",sslipi," ssgradlipi",ssgradlipi
+#endif
+      return
+      end subroutine lipid_layer
 
 
+!-------------------------------------------------------------------------- 
+!--------------------------------------------------------------------------
       end module energy
       end module energy
UNRESPACK 4.x