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 38aaba2..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)
  
  
@@ -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
  
@@ -333,6 +334,7 @@
            weights_(47)=wpepbase
            weights_(48)=wscpho
            weights_(49)=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)
  
@@ -381,6 +383,7 @@
            wpepbase=weights(47)
            wscpho=weights(48)
            wpeppho=weights(49)
            wpepbase=weights(47)
            wscpho=weights(48)
            wpeppho=weights(49)
+          wcatnucl=weights(50)
  !      welpsb=weights(28)*fact(1)
  !
  !      wcorr_nucl= weights(37)*fact(1)
  !      welpsb=weights(28)*fact(1)
  !
  !      wcorr_nucl= weights(37)*fact(1)
@@ -397,9 +400,15 @@
          if (nfgtasks.gt.1) then 
          call MPI_Bcast(itime_mat,1,MPI_INT,king,FG_COMM,IERROR)
          endif
          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
         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
         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
         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
  
  !      print *,'Processor',myrank,' calling etotal ipot=',ipot
  !      print *,'Processor',myrank,' nnt=',nnt,' nct=',nct
@@ -837,6 +846,7 @@
        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
        else
         etors_nucl=0.0d0
         estr_nucl=0.0d0
@@ -851,6 +861,7 @@
         evdwpp=0.0d0
         eespp=0.0d0
         etors_d_nucl=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
@@ -954,6 +965,7 @@
        energia(48)=escpho
        energia(49)=epeppho
  !      energia(50)=ecations_prot_amber
        energia(48)=escpho
        energia(49)=epeppho
  !      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"
@@ -996,7 +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
@@ -1080,6 +1093,7 @@
        epepbase=energia(47)
        escpho=energia(48)
        epeppho=energia(49)
        epepbase=energia(47)
        escpho=energia(48)
        epeppho=energia(49)
+      ecation_nucl=energia(50)
  !      ecations_prot_amber=energia(50)
  
  !      energia(41)=ecation_prot
  !      ecations_prot_amber=energia(50)
  
  !      energia(41)=ecation_prot
@@ -1099,7 +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
+       +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 &
@@ -1113,7 +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
+       +wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho+wcatnucl*ecation_nucl
  #endif
        energia(0)=etot
  ! detecting NaNQ
  #endif
        energia(0)=etot
  ! detecting NaNQ
@@ -1246,7 +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)
@@ -1300,6 +1315,7 @@
        epepbase=energia(47)
        escpho=energia(48)
        epeppho=energia(49)
        epepbase=energia(47)
        escpho=energia(48)
        epeppho=energia(49)
+      ecation_nucl=energia(50)
  !      ecations_prot_amber=energia(50)
  #ifdef SPLITELE
        write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp,&
  !      ecations_prot_amber=energia(50)
  #ifdef SPLITELE
        write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp,&
@@ -1316,7 +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,&
-        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)'/ &
@@ -1363,6 +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,&
@@ -1379,7 +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,&
-        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)'/ &
@@ -1425,6 +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
@@ -1898,12 +1916,12 @@
        dCAVdOM1=0.0d0 
        dGCLdOM1=0.0d0 
        dPOLdOM1=0.0d0
        dCAVdOM1=0.0d0 
        dGCLdOM1=0.0d0 
        dPOLdOM1=0.0d0
-
-
+!             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)
        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))
  !      do i=iatsc_s,iatsc_e
  !C        print *,"I am in EVDW",i
          itypi=iabs(itype(i,1))
@@ -1935,7 +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
@@ -1991,6 +2009,7 @@
             zj=c(3,nres+j)
                call to_box(xj,yj,zj)
                call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
             zj=c(3,nres+j)
                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 &
                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 &
@@ -3431,6 +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
@@ -4682,36 +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
@@ -4925,8 +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)
@@ -4944,30 +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
@@ -5086,14 +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
@@ -5419,6 +5402,7 @@
  !d    print '(a)','Enter ESCP'
  !d    write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
  !      do i=iatscp_s,iatscp_e
  !d    print '(a)','Enter ESCP'
  !d    write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',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)
         do icont=g_listscp_start,g_listscp_end
          i=newcontlistscpi(icont)
          j=newcontlistscpj(icont)
@@ -5445,12 +5429,6 @@
            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
  
            call to_box(xj,yj,zj)
            xj=boxshift(xj-xi,boxxsize)
  
            call to_box(xj,yj,zj)
            xj=boxshift(xj-xi,boxxsize)
@@ -5586,7 +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
@@ -5715,6 +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)
@@ -5723,9 +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)
@@ -5750,9 +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
@@ -11184,7 +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)
  
         
  
  
         
  
@@ -11222,7 +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
@@ -11463,7 +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)
  
  
  
  
  
  
@@ -11490,7 +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
@@ -11786,7 +11770,7 @@
        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)
         enddo
  !       print *,i,j,gg_lipi(3),gg_lipj(3),sss_ele_cut
  !      write (iout,*) "gg",(gg(k),k=1,3)
@@ -12542,6 +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
@@ -12766,12 +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
@@ -13427,6 +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.
  !
@@ -13437,6 +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
@@ -16362,7 +16362,7 @@ chip1=chip(itypi)
  ! 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
@@ -16382,14 +16382,14 @@ chip1=chip(itypi)
  !
        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)
@@ -16416,13 +16416,13 @@ chip1=chip(itypi)
        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)
@@ -16439,15 +16439,15 @@ chip1=chip(itypi)
  ! 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
@@ -16487,9 +16487,9 @@ chip1=chip(itypi)
        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
@@ -16499,11 +16499,11 @@ chip1=chip(itypi)
        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
@@ -16514,7 +16514,7 @@ chip1=chip(itypi)
        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
@@ -16528,10 +16528,10 @@ chip1=chip(itypi)
          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
@@ -16606,18 +16606,18 @@ chip1=chip(itypi)
        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
@@ -16715,12 +16715,13 @@ chip1=chip(itypi)
  !      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
@@ -16774,8 +16775,8 @@ chip1=chip(itypi)
  !          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
@@ -16792,7 +16793,7 @@ chip1=chip(itypi)
              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
@@ -16812,24 +16813,24 @@ chip1=chip(itypi)
              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'
@@ -16839,7 +16840,7 @@ chip1=chip(itypi)
        !      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)
@@ -16873,114 +16874,116 @@ chip1=chip(itypi)
        !      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.
@@ -16993,42 +16996,42 @@ chip1=chip(itypi)
        !      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' 
@@ -17039,19 +17042,19 @@ chip1=chip(itypi)
        !      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
@@ -17067,545 +17070,608 @@ chip1=chip(itypi)
  
  
  #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
-              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
+          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).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
+          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
-#endif
+          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
  !#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'
@@ -17614,37 +17680,37 @@ chip1=chip(itypi)
        !      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),&
@@ -17658,23 +17724,23 @@ chip1=chip(itypi)
        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),&
@@ -17690,27 +17756,27 @@ chip1=chip(itypi)
         "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),&
@@ -17726,27 +17792,27 @@ chip1=chip(itypi)
         "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),&
@@ -17783,53 +17849,53 @@ chip1=chip(itypi)
        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
@@ -17856,97 +17922,97 @@ chip1=chip(itypi)
  !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
+      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
              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)
-          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
+            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
              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
+      enddo       
         else
         else
-        do il=seg1,seg2
-        if((seg3-il).lt.3) then
-             secseg=il+3
-        else
-             secseg=seg3
-        endif 
-          do jl=secseg,seg4
+      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
              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)
+            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
              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
+      enddo                   
        endif
        enddo
         do i=0,nres
        endif
        enddo
         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
@@ -17967,24 +18033,24 @@ chip1=chip(itypi)
        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
@@ -18020,26 +18086,26 @@ chip1=chip(itypi)
  !      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              
@@ -18047,8 +18113,8 @@ chip1=chip(itypi)
  !     &   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)
@@ -18061,22 +18127,22 @@ chip1=chip(itypi)
  !        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              
@@ -18084,8 +18150,8 @@ chip1=chip(itypi)
  !     &   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)
@@ -18098,27 +18164,27 @@ chip1=chip(itypi)
  !        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
@@ -18163,95 +18229,95 @@ chip1=chip(itypi)
  !     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
@@ -18300,10 +18366,10 @@ chip1=chip(itypi)
        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
@@ -18316,27 +18382,27 @@ chip1=chip(itypi)
  !        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
@@ -18466,8 +18532,8 @@ chip1=chip(itypi)
        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
@@ -18489,119 +18555,119 @@ chip1=chip(itypi)
  !-------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
@@ -18673,9 +18739,9 @@ chip1=chip(itypi)
  !        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)')
@@ -18686,35 +18752,35 @@ chip1=chip(itypi)
  
  !-------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
@@ -18723,14 +18789,14 @@ chip1=chip(itypi)
  !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
@@ -18788,11 +18854,12 @@ chip1=chip(itypi)
        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)
@@ -18801,7 +18868,7 @@ chip1=chip(itypi)
        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)
@@ -18852,47 +18919,47 @@ chip1=chip(itypi)
  !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
@@ -18958,7 +19025,7 @@ chip1=chip(itypi)
        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
@@ -18967,78 +19034,78 @@ chip1=chip(itypi)
  
        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
  
@@ -19047,45 +19114,44 @@ chip1=chip(itypi)
  !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
@@ -19106,45 +19172,45 @@ chip1=chip(itypi)
  !      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
@@ -19152,9 +19218,9 @@ chip1=chip(itypi)
         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)
@@ -19162,37 +19228,37 @@ chip1=chip(itypi)
         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
@@ -19216,8 +19282,8 @@ chip1=chip(itypi)
        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
@@ -19228,22 +19294,22 @@ chip1=chip(itypi)
        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)
@@ -19271,46 +19337,46 @@ chip1=chip(itypi)
  !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),
@@ -19336,19 +19402,19 @@ chip1=chip(itypi)
         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)
@@ -19370,15 +19436,15 @@ chip1=chip(itypi)
  !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 
@@ -19394,23 +19460,23 @@ chip1=chip(itypi)
  !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)
@@ -19432,140 +19498,140 @@ chip1=chip(itypi)
  !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
@@ -19583,28 +19649,28 @@ chip1=chip(itypi)
         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
@@ -19617,8 +19683,8 @@ chip1=chip(itypi)
        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 
@@ -19631,32 +19697,32 @@ chip1=chip(itypi)
        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
@@ -19687,72 +19753,72 @@ chip1=chip(itypi)
  !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
@@ -19780,46 +19846,46 @@ chip1=chip(itypi)
  !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
@@ -19838,8 +19904,8 @@ chip1=chip(itypi)
  !         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
  
  !===============================================
  !--------------------------------------------------------------------------------
  
  !===============================================
  !--------------------------------------------------------------------------------
@@ -19847,24 +19913,24 @@ chip1=chip(itypi)
  
         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
@@ -19895,40 +19961,40 @@ chip1=chip(itypi)
         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))
@@ -19943,7 +20009,7 @@ chip1=chip(itypi)
  !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 !
@@ -19965,17 +20031,17 @@ chip1=chip(itypi)
  !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)- &
@@ -19984,37 +20050,37 @@ chip1=chip(itypi)
         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
@@ -20095,9 +20161,9 @@ chip1=chip(itypi)
        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
@@ -20108,16 +20174,16 @@ chip1=chip(itypi)
  !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
  !-----------------------------------------------------------------------------
@@ -20129,11 +20195,11 @@ chip1=chip(itypi)
        integer :: i,j
        
        if(nres.lt.100) then
        integer :: i,j
        
        if(nres.lt.100) then
-        maxconts=10*nres
+      maxconts=10*nres
        elseif(nres.lt.200) then
        elseif(nres.lt.200) then
-        maxconts=10*nres      ! Max. number of contacts per residue
+      maxconts=10*nres      ! Max. number of contacts per residue
        else
        else
-        maxconts=10*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
@@ -20379,6 +20445,8 @@ chip1=chip(itypi)
        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))
@@ -20507,7 +20575,7 @@ chip1=chip(itypi)
  !      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
@@ -20562,12 +20630,12 @@ chip1=chip(itypi)
        allocate(uzgrad(3,3,2,nres))
  !(3,3,2,maxres)
  ! allocateion of lists JPRDLA
        allocate(uzgrad(3,3,2,nres))
  !(3,3,2,maxres)
  ! allocateion of lists JPRDLA
-      allocate(newcontlistppi(200*nres))
-      allocate(newcontlistscpi(200*nres))
-      allocate(newcontlisti(200*nres))
-      allocate(newcontlistppj(200*nres))
-      allocate(newcontlistscpj(200*nres))
-      allocate(newcontlistj(200*nres))
+      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
@@ -20587,8 +20655,8 @@ chip1=chip(itypi)
        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)
@@ -20598,14 +20666,14 @@ chip1=chip(itypi)
  !     &       "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
@@ -20617,50 +20685,50 @@ chip1=chip(itypi)
  
        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
@@ -20682,168 +20750,168 @@ chip1=chip(itypi)
        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
@@ -20868,61 +20936,61 @@ chip1=chip(itypi)
  !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
@@ -20937,12 +21005,13 @@ chip1=chip(itypi)
  !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
@@ -20957,124 +21026,87 @@ chip1=chip(itypi)
  !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
@@ -21091,9 +21123,9 @@ chip1=chip(itypi)
        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'
@@ -21102,23 +21134,18 @@ chip1=chip(itypi)
        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
+      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 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
+      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
@@ -21127,79 +21154,48 @@ chip1=chip(itypi)
  !          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
+        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)
  
  
-          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"
+      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
@@ -21212,7 +21208,7 @@ chip1=chip(itypi)
        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
@@ -21223,160 +21219,127 @@ chip1=chip(itypi)
        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.
@@ -21389,7 +21352,7 @@ chip1=chip(itypi)
        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
@@ -21398,13 +21361,13 @@ chip1=chip(itypi)
        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)
@@ -21428,13 +21391,13 @@ chip1=chip(itypi)
  !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
@@ -21456,12 +21419,12 @@ chip1=chip(itypi)
        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
@@ -21479,10 +21442,10 @@ chip1=chip(itypi)
        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
@@ -21497,123 +21460,123 @@ chip1=chip(itypi)
        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.maxcont) 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_nucl(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.',maxconts
-          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
@@ -21626,26 +21589,26 @@ chip1=chip(itypi)
        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
@@ -21670,126 +21633,126 @@ chip1=chip(itypi)
        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))
@@ -21797,45 +21760,45 @@ chip1=chip(itypi)
         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",
@@ -21846,12 +21809,12 @@ chip1=chip(itypi)
  !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),
@@ -21874,8 +21837,8 @@ chip1=chip(itypi)
  !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
@@ -21907,12 +21870,12 @@ chip1=chip(itypi)
  
        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!
@@ -21920,9 +21883,9 @@ chip1=chip(itypi)
        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
@@ -21931,33 +21894,33 @@ chip1=chip(itypi)
  !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
@@ -21972,24 +21935,24 @@ chip1=chip(itypi)
  !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
@@ -21997,18 +21960,18 @@ chip1=chip(itypi)
  !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.
@@ -22016,12 +21979,12 @@ chip1=chip(itypi)
     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
@@ -22037,17 +22000,17 @@ chip1=chip(itypi)
  !      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.
@@ -22055,11 +22018,11 @@ chip1=chip(itypi)
  !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.
@@ -22069,20 +22032,20 @@ chip1=chip(itypi)
  !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
@@ -22099,9 +22062,9 @@ chip1=chip(itypi)
  !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)
@@ -22130,32 +22093,32 @@ chip1=chip(itypi)
        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
@@ -22174,9 +22137,9 @@ chip1=chip(itypi)
  !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)
@@ -22204,32 +22167,32 @@ chip1=chip(itypi)
        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
@@ -22240,16 +22203,16 @@ chip1=chip(itypi)
        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
@@ -22267,133 +22230,99 @@ chip1=chip(itypi)
        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,itypi,itypj
-        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
+      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
  !        k0 = 332.0*(2.0*2.0)/80.0
-        itmp=0
-        
-        do i=1,4
-        itmp=itmp+nres_molec(i)
-        enddo
+      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=c(1,i)
+      yi=c(2,i)
+      zi=c(3,i)
  !        write (iout,*) i,"TUTUT",c(1,i)
  !        write (iout,*) i,"TUTUT",c(1,i)
-          itypi=itype(i,5)
-          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)
-          itypj=itype(j,5)
+        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
  !          print *,i,j,itypi,itypj
-          k0 = 332.0*(ichargecat(itypi)*ichargecat(itypj))/80.0
+        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
-        if (energy_dec) write (iout,*) i,j,Evan1cat,Evan2cat,Eeleccat,&
-         r012,rcal**6,ichargecat(itypi)*ichargecat(itypj)
+      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 
         enddo
         enddo
         return 
@@ -22409,10 +22338,10 @@ chip1=chip(itypi)
  !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
@@ -22429,120 +22358,100 @@ chip1=chip(itypi)
        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
  
        evdw=0.0D0
        if (nres_molec(5).eq.0) return
        eps_out=80.0d0
  !      sss_ele_cut=1.0d0
  
  
        evdw=0.0D0
        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
  !        go to 17
  !        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).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)
-          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,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)
-           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 = chi1cat(itypi,itypj)
-          chis1 = chis1cat(itypi,itypj)
-          chip1 = chipp1cat(itypi,itypj)
+        chi1 = chi1cat(itypi,itypj)
+        chis1 = chis1cat(itypi,itypj)
+        chip1 = chipp1cat(itypi,itypj)
  !          chi1=0.0d0
  !          chis1=0.0d0
  !          chip1=0.0d0
  !          chi1=0.0d0
  !          chis1=0.0d0
  !          chip1=0.0d0
-          chi2=0.0
-          chip2=0.0
-          chis2=0.0
+        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
@@ -22551,18 +22460,20 @@ chip1=chip(itypi)
  !       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)
@@ -22571,18 +22482,23 @@ chip1=chip(itypi)
  ! 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
@@ -22597,48 +22513,59 @@ chip1=chip(itypi)
         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_cat(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_cat(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
@@ -22646,120 +22573,111 @@ chip1=chip(itypi)
  !           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) )
         facd1 = dtailcat(1,itypi,itypj) * vbld_inv(i+nres)
         END DO
         erdxi = scalar( ertail(1), dC_norm(1,i+nres) )
         erdxj = scalar( ertail(1), dC_norm(1,j) )
         facd1 = dtailcat(1,itypi,itypj) * vbld_inv(i+nres)
-       facd2 = dtailcat(2,itypi,itypj) * vbld_inv(j+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))
-        gradpepcatx(k,i) = gradpepcatx(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)
-        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
+      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
         ENDDO
  !c! Compute head-head and head-tail energies for each state
-          isel = iabs(Qi) + 1 ! ion is always charged so  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) 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) 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
-           write(iout,*) "KURWA0",d1
+        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
+         CALL edq_cat(ecl, elj, epol)
+        eheadtail = ECL + elj + epol
  !           eheadtail = 0.0d0
  
  !           eheadtail = 0.0d0
  
-          ELSE IF ((isel.eq.2)) 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.  &
@@ -22777,128 +22695,104 @@ chip1=chip(itypi)
  !
  !           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
-        evdw = evdw  + Fcav + eheadtail
+       else
+       write(iout,*) "not yet implemented",j,itype(j,5)
+       endif
+!!       endif ! turn off electrostatic
+      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
  !       evdw = evdw  + Fcav  + eheadtail
-
+!       print *,"before sc_grad_cat", i,j, gradpepcat(1,j) 
  !        iF (nstate(itypi,itypj).eq.1) THEN
  !        iF (nstate(itypi,itypj).eq.1) THEN
-        CALL sc_grad_cat
+      CALL sc_grad_cat
+!       print *,"after sc_grad_cat", i,j, gradpepcat(1,j)
+
  !       END IF
  !c!-------------------------------------------------------------------
  !c! NAPISY KONCOWE
  !       END IF
  !c!-------------------------------------------------------------------
  !c! NAPISY KONCOWE
-         END DO   ! j
+       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
         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
-        do i=ibond_start,ibond_end
+!      go to 23
+      do i=ibond_start,ibond_end
  
  !        print *,"I am in EVDW",i
  
  !        print *,"I am in EVDW",i
-        itypi=10 ! the peptide group parameters are for glicine
+      itypi=10 ! the peptide group parameters are for glicine
    
  !        if (i.ne.47) cycle
    
  !        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
-          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,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)
+      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.
  
  ! 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)
-           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_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)
  
  
-          dxj = 0.0d0! dc_norm( 1, nres+j )
-          dyj = 0.0d0!dc_norm( 2, nres+j )
-          dzj = 0.0d0! dc_norm( 3, nres+j )
+        dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
  
  
-          itypi = 10
-          itypj = itype(j,5)
+        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)
  ! 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 = chi1cat(itypi,itypj)
+        chis1 = chis1cat(itypi,itypj)
+        chip1 = chipp1cat(itypi,itypj)
  !          chi1=0.0d0
  !          chis1=0.0d0
  !          chip1=0.0d0
  !          chi1=0.0d0
  !          chis1=0.0d0
  !          chip1=0.0d0
-          chi2=0.0
-          chip2=0.0
-          chis2=0.0
+        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)
+        
  ! 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
@@ -22907,18 +22801,23 @@ chip1=chip(itypi)
  !       Rtail = 0.0d0
  
         DO k = 1, 3
  !       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)
+      ctail(k,1)=(c(k,i)+c(k,i+1))/2.0
+      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)
+       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)
  !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 = 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)
@@ -22929,18 +22828,27 @@ chip1=chip(itypi)
  ! 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)+c(k,i+1))/2.0 + d1 * dc_norm(k, i)
-        chead(k,2) = c(k, j)
+      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)
  ! 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)
+      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
         END DO
+
  ! pitagoras (root of sum of squares)
         Rhead = dsqrt( &
  ! 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
@@ -22955,48 +22863,55 @@ chip1=chip(itypi)
         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)
-          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_cat(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),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
  !          print *,"ADAM",aa_aq(itypi,itypj)
  
  !          c1        = 0.0d0
-          c2        = fac  * bb_aq_cat(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
@@ -23004,109 +22919,112 @@ chip1=chip(itypi)
  !           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
+        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
+        fac = chis1 * sqom1 + chis2 * sqom2 &
+        - 2.0d0 * chis12 * om1 * om2 * om12
+        
+        pom = 1.0d0 - chis1 * chis2 * sqom12
  !          print *,"TUT2",fac,chis1,sqom1,pom
  !          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
+        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) )
         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
         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))
+      pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i))
  !        gradpepcatx(k,i) = gradpepcatx(k,i) &
  !                  - (( dFdR + gg(k) ) * pom)
  !        gradpepcatx(k,i) = gradpepcatx(k,i) &
  !                  - (( dFdR + gg(k) ) * pom)
-        pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres))
+      pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres))
  !        gvdwx(k,j) = gvdwx(k,j)   &
  !                  + (( dFdR + gg(k) ) * pom)
  !        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
+      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
         ENDDO
+      if (itype(j,5).gt.0) then
  !c! Compute head-head and head-tail energies for each state
  !c! Compute head-head and head-tail energies for each state
-          isel = 3
+        isel = 3
  !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_pep(ecl, elj, epol)
-           eheadtail = ECL + elj + epol
+         CALL edq_cat_pep(ecl, elj, epol)
+         eheadtail = ECL + elj + epol
  !          print *,"i,",i,eheadtail
  !           eheadtail = 0.0d0
  !          print *,"i,",i,eheadtail
  !           eheadtail = 0.0d0
-
-        evdw = evdw  + Fcav + eheadtail
-
+      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)') &
         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
  
  !        iF (nstate(itypi,itypj).eq.1) THEN
  !       evdw = evdw  + Fcav  + eheadtail
  
  !        iF (nstate(itypi,itypj).eq.1) THEN
-        CALL sc_grad_cat_pep
+      CALL sc_grad_cat_pep
  !       END IF
  !c!-------------------------------------------------------------------
  !c! NAPISY KONCOWE
  !       END IF
  !c!-------------------------------------------------------------------
  !c! NAPISY KONCOWE
-         END DO   ! j
+       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
@@ -23117,109 +23035,69 @@ chip1=chip(itypi)
  !      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)
-!           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
-!        itmp=0
+       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)
  
  
-           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
+       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
+       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
+
+         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
  !       enddo
  !       enddo
         rcpm = sqrt(xj**2+yj**2+zj**2)
  !       enddo
  !       enddo
         rcpm = sqrt(xj**2+yj**2+zj**2)
@@ -23232,498 +23110,675 @@ chip1=chip(itypi)
         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)
@@ -23747,128 +23802,96 @@ chip1=chip(itypi)
        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)
@@ -23881,18 +23904,18 @@ chip1=chip(itypi)
  ! 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
@@ -23907,95 +23930,95 @@ chip1=chip(itypi)
         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 &
@@ -24009,30 +24032,30 @@ chip1=chip(itypi)
         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
@@ -24041,7 +24064,7 @@ chip1=chip(itypi)
  
  !          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)
@@ -24050,9 +24073,9 @@ chip1=chip(itypi)
         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
@@ -24071,20 +24094,20 @@ chip1=chip(itypi)
  !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
@@ -24093,7 +24116,7 @@ chip1=chip(itypi)
         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) )
@@ -24101,17 +24124,17 @@ chip1=chip(itypi)
         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
@@ -24128,7 +24151,7 @@ chip1=chip(itypi)
         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)
@@ -24143,12 +24166,12 @@ chip1=chip(itypi)
         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
@@ -24164,20 +24187,20 @@ chip1=chip(itypi)
         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) )
@@ -24190,31 +24213,31 @@ chip1=chip(itypi)
  !       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
@@ -24222,7 +24245,7 @@ chip1=chip(itypi)
  !       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
@@ -24232,44 +24255,44 @@ chip1=chip(itypi)
  
         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
@@ -24283,144 +24306,106 @@ chip1=chip(itypi)
        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
@@ -24434,118 +24419,118 @@ chip1=chip(itypi)
         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
@@ -24562,29 +24547,29 @@ chip1=chip(itypi)
         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 
@@ -24594,7 +24579,7 @@ chip1=chip(itypi)
         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) )
@@ -24606,19 +24591,19 @@ chip1=chip(itypi)
  !+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
@@ -24631,28 +24616,28 @@ chip1=chip(itypi)
  
         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)
@@ -24662,24 +24647,24 @@ chip1=chip(itypi)
  !       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
@@ -24702,124 +24687,92 @@ chip1=chip(itypi)
  !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
         integer troll
         eps_out=80.0d0
         escpho=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
         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
+      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)
@@ -24828,24 +24781,24 @@ chip1=chip(itypi)
  !       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
@@ -24862,104 +24815,104 @@ chip1=chip(itypi)
         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 )
@@ -24971,20 +24924,20 @@ chip1=chip(itypi)
  !                 +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)
@@ -24995,7 +24948,7 @@ chip1=chip(itypi)
         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)
@@ -25016,15 +24969,15 @@ chip1=chip(itypi)
         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
@@ -25037,7 +24990,7 @@ chip1=chip(itypi)
         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)
@@ -25053,25 +25006,25 @@ chip1=chip(itypi)
         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) )
@@ -25084,38 +25037,38 @@ chip1=chip(itypi)
  !       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
@@ -25123,10 +25076,10 @@ chip1=chip(itypi)
         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
  
@@ -25137,28 +25090,28 @@ chip1=chip(itypi)
  
         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)
@@ -25168,20 +25121,20 @@ chip1=chip(itypi)
  !       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)),&
@@ -25189,7 +25142,7 @@ chip1=chip(itypi)
  !        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
@@ -25214,118 +25167,83 @@ chip1=chip(itypi)
        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
@@ -25340,27 +25258,27 @@ chip1=chip(itypi)
         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
@@ -25379,13 +25297,13 @@ chip1=chip(itypi)
         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
@@ -25393,32 +25311,32 @@ chip1=chip(itypi)
         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
@@ -25445,21 +25363,21 @@ chip1=chip(itypi)
  !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
  !       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
@@ -25471,72 +25389,46 @@ chip1=chip(itypi)
  !       print *,"EVDW KURW",evdw,nres
        do i=iatsc_s,iatsc_e
  !        print *,"I am in EVDW",i
  !       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
@@ -25544,64 +25436,36 @@ chip1=chip(itypi)
  !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
@@ -25614,17 +25478,17 @@ chip1=chip(itypi)
  !          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
@@ -25633,23 +25497,23 @@ chip1=chip(itypi)
  !          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)
@@ -25657,9 +25521,9 @@ chip1=chip(itypi)
         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
  !-------------------------------------------------------------------
@@ -25671,18 +25535,18 @@ chip1=chip(itypi)
  ! 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
@@ -25697,49 +25561,49 @@ chip1=chip(itypi)
         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
@@ -25747,60 +25611,60 @@ chip1=chip(itypi)
  !           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) )
@@ -25809,24 +25673,24 @@ chip1=chip(itypi)
         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
@@ -25834,7 +25698,7 @@ chip1=chip(itypi)
  
  !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
@@ -25846,123 +25710,123 @@ chip1=chip(itypi)
  !           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.
@@ -25975,7 +25839,7 @@ chip1=chip(itypi)
        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)
@@ -25986,8 +25850,8 @@ chip1=chip(itypi)
         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)
@@ -25998,8 +25862,8 @@ chip1=chip(itypi)
         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)
@@ -26022,13 +25886,13 @@ chip1=chip(itypi)
         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!-------------------------------------------------------------------
@@ -26067,17 +25931,17 @@ chip1=chip(itypi)
        (( 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
@@ -26093,7 +25957,7 @@ chip1=chip(itypi)
         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
@@ -26101,9 +25965,9 @@ chip1=chip(itypi)
  !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) )
@@ -26119,43 +25983,43 @@ chip1=chip(itypi)
  
  !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
@@ -26165,19 +26029,19 @@ chip1=chip(itypi)
        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)
@@ -26188,8 +26052,8 @@ chip1=chip(itypi)
         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)
@@ -26212,13 +26076,13 @@ chip1=chip(itypi)
         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!-------------------------------------------------------------------
@@ -26257,17 +26121,17 @@ chip1=chip(itypi)
        (( 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
@@ -26283,7 +26147,7 @@ chip1=chip(itypi)
         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
@@ -26291,9 +26155,9 @@ chip1=chip(itypi)
  !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) )
@@ -26309,43 +26173,43 @@ chip1=chip(itypi)
  
  !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))
-        gradpepcatx(k,i) = gradpepcatx(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
+              - dGLJdR * pom
  
  
-        pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j))
+      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
  
  !        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)
+      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
@@ -26373,7 +26237,7 @@ chip1=chip(itypi)
         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)
@@ -26382,34 +26246,34 @@ chip1=chip(itypi)
  !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
@@ -26418,54 +26282,54 @@ chip1=chip(itypi)
         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
@@ -26477,207 +26341,207 @@ chip1=chip(itypi)
  !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
@@ -26698,7 +26562,7 @@ chip1=chip(itypi)
         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)
@@ -26716,19 +26580,19 @@ chip1=chip(itypi)
         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))
@@ -26736,17 +26600,17 @@ chip1=chip(itypi)
         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
@@ -26760,7 +26624,7 @@ chip1=chip(itypi)
         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)
@@ -26777,13 +26641,13 @@ chip1=chip(itypi)
         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
@@ -26793,26 +26657,26 @@ chip1=chip(itypi)
  !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
@@ -26822,12 +26686,12 @@ chip1=chip(itypi)
        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)
@@ -26844,13 +26708,13 @@ chip1=chip(itypi)
         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
@@ -26861,26 +26725,26 @@ chip1=chip(itypi)
  !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)))
  
-        gradpepcatx(k,i) = gradpepcatx(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)))
  !        gradpepcatx(k,j) = gradpepcatx(k,j)   &
  !                   + dPOLdR2 * condor
  
         -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))
  !        gradpepcatx(k,j) = gradpepcatx(k,j)   &
  !                   + dPOLdR2 * condor
  
-        gradpepcat(k,i) = gradpepcat(k,i) &
-                   - dPOLdR2 * erhead_tail(k,2)
-        gradpepcat(k,j) = gradpepcat(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
@@ -26900,7 +26764,7 @@ chip1=chip(itypi)
         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)
@@ -26915,9 +26779,9 @@ chip1=chip(itypi)
         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
@@ -26934,13 +26798,13 @@ chip1=chip(itypi)
  !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
@@ -26952,11 +26816,11 @@ chip1=chip(itypi)
         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) )
@@ -26968,32 +26832,32 @@ chip1=chip(itypi)
         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
@@ -27014,7 +26878,7 @@ chip1=chip(itypi)
         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)
@@ -27030,12 +26894,12 @@ chip1=chip(itypi)
         sparrow  = w1 * Qj * om1
         hawk     = w2 * Qj * Qj * (1.0d0 - sqom2)
         ECL = sparrow / Rhead**2.0d0 &
         sparrow  = w1 * Qj * om1
         hawk     = w2 * Qj * Qj * (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 * Qj) / (Rhead**2.0d0)
  !c! dF/dom2
  !c! dF/dom1
         dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
  !c! dF/dom2
@@ -27049,13 +26913,13 @@ chip1=chip(itypi)
         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
@@ -27067,14 +26931,14 @@ chip1=chip(itypi)
         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) )
@@ -27084,32 +26948,32 @@ chip1=chip(itypi)
         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))) &
         -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+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,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)
+      gvdwc(k,j) = gvdwc(k,j) &
+              + dGCLdR * erhead(k) &
+              + dPOLdR2 * erhead_tail(k,2) &
+              + dGLJdR * erhead(k)
  
         END DO
         RETURN
  
         END DO
         RETURN
@@ -27120,7 +26984,7 @@ chip1=chip(itypi)
        use calc_data
  
        double precision  facd3, adler,ecl,elj,epol
        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)
@@ -27130,7 +26994,7 @@ chip1=chip(itypi)
         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)
@@ -27143,16 +27007,16 @@ chip1=chip(itypi)
  
  !c!-------------------------------------------------------------------
  !c! ecl
  
  !c!-------------------------------------------------------------------
  !c! ecl
-       write(iout,*) "KURWA2",Rhead
+!       write(iout,*) "KURWA2",Rhead
         sparrow  = w1 * Qj * om1
         hawk     = w2 * Qj * Qj * (1.0d0 - sqom2)
         ECL = sparrow / Rhead**2.0d0 &
         sparrow  = w1 * Qj * om1
         hawk     = w2 * Qj * Qj * (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 * Qj) / (Rhead**2.0d0)
  !c! dF/dom2
  !c! dF/dom1
         dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
  !c! dF/dom2
@@ -27167,13 +27031,13 @@ chip1=chip(itypi)
         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
@@ -27185,15 +27049,15 @@ chip1=chip(itypi)
         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) )
         END DO
         erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
         erdxj = scalar( erhead(1), dC_norm(1,j) )
@@ -27203,32 +27067,32 @@ chip1=chip(itypi)
         facd2 = d2 * vbld_inv(j)
         facd3 = dtailcat(1,itypi,itypj) * vbld_inv(i+nres)
         DO k = 1, 3
         facd2 = d2 * vbld_inv(j)
         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)))
  
-        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) &
+      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))
+      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j))
  !        gradpepcatx(k,j) = gradpepcatx(k,j) &
  !                  + dGCLdR * pom &
  !                  + dPOLdR2 * condor &
  !                  + dGLJdR * pom
  
  
  !        gradpepcatx(k,j) = gradpepcatx(k,j) &
  !                  + dGCLdR * pom &
  !                  + dPOLdR2 * condor &
  !                  + dGLJdR * pom
  
  
-        gradpepcat(k,i) = gradpepcat(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)
  
  
-        gradpepcat(k,j) = gradpepcat(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
@@ -27239,7 +27103,7 @@ chip1=chip(itypi)
        use calc_data
  
        double precision  facd3, adler,ecl,elj,epol
        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)
@@ -27249,7 +27113,7 @@ chip1=chip(itypi)
         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)
@@ -27267,12 +27131,12 @@ chip1=chip(itypi)
  !       print *,"CO2", itypi,itypj
  !       print *,"CO?!.", w1,w2,Qj,om1
         ECL = sparrow / Rhead**2.0d0 &
  !       print *,"CO2", itypi,itypj
  !       print *,"CO?!.", w1,w2,Qj,om1
         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 * Qj) / (Rhead**2.0d0)
  !c! dF/dom2
  !c! dF/dom1
         dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
  !c! dF/dom2
@@ -27287,13 +27151,13 @@ chip1=chip(itypi)
         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
@@ -27305,15 +27169,15 @@ chip1=chip(itypi)
         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) )
         erdxj = scalar( erhead(1), dC_norm(1,j) )
         END DO
         erdxi = scalar( erhead(1), dC_norm(1,i) )
         erdxj = scalar( erhead(1), dC_norm(1,j) )
@@ -27323,37 +27187,37 @@ chip1=chip(itypi)
         facd2 = d2 * vbld_inv(j)
         facd3 = dtailcat(1,itypi,itypj) * vbld_inv(i+1)/2.0
         DO k = 1, 3
         facd2 = d2 * vbld_inv(j)
         facd3 = dtailcat(1,itypi,itypj) * vbld_inv(i+1)/2.0
         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))
+      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
  
  !        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))
+      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j))
  !        gradpepcatx(k,j) = gradpepcatx(k,j) &
  !                  + dGCLdR * pom &
  !                  + dPOLdR2 * condor &
  !                  + dGLJdR * pom
  
  
  !        gradpepcatx(k,j) = gradpepcatx(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))
+      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))
  
  
  
  
-        gradpepcat(k,j) = gradpepcat(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
@@ -27373,7 +27237,7 @@ chip1=chip(itypi)
         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
@@ -27392,17 +27256,17 @@ chip1=chip(itypi)
  !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)
@@ -27412,7 +27276,7 @@ chip1=chip(itypi)
  !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) )
@@ -27420,13 +27284,13 @@ chip1=chip(itypi)
         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
@@ -27507,8 +27371,8 @@ chip1=chip(itypi)
  !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)
@@ -27516,9 +27380,9 @@ chip1=chip(itypi)
         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
@@ -27530,18 +27394,18 @@ chip1=chip(itypi)
  !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
@@ -27585,9 +27449,9 @@ chip1=chip(itypi)
         alf1   = 0.0d0
         alf2   = 0.0d0
         alf12  = 0.0d0
         alf1   = 0.0d0
         alf2   = 0.0d0
         alf12  = 0.0d0
-       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! distance from center of chain(?) to polar/charged head
         d1 = dheadcat(1, 1, itypi, itypj)
         d2 = dheadcat(2, 1, itypi, itypj)
@@ -27617,8 +27481,8 @@ chip1=chip(itypi)
  !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)!-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)
@@ -27626,9 +27490,9 @@ chip1=chip(itypi)
         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
@@ -27640,18 +27504,18 @@ chip1=chip(itypi)
  !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) 
+      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
@@ -27726,8 +27590,8 @@ chip1=chip(itypi)
  !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)+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)
+      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)
         END DO
  !c! tail distances will be themselves usefull elswhere
  !c1 (in Gcav, for example)
@@ -27735,9 +27599,9 @@ chip1=chip(itypi)
         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
@@ -27749,18 +27613,18 @@ chip1=chip(itypi)
  !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)+c(k,i+1))/2.0 + d1 * dc_norm(k, i)
-        chead(k,2) = c(k, j) 
+      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)
  !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
@@ -27787,11 +27651,11 @@ chip1=chip(itypi)
        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
@@ -27807,11 +27671,11 @@ chip1=chip(itypi)
        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
  !C        print *, x(i+1),yy(i),i
        enddo
        gradtschebyshev=aux
@@ -27822,81 +27686,49 @@ chip1=chip(itypi)
        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
        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(200*nres),contlistj(200*nres)
+      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"
  !      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)
-             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
-             do iint=1,nint_gr(i)
-              do j=istart(i,iint),iend(i,iint)
-               itypj=iabs(itype(j,1))
-               if (itypj.eq.ntyp1) cycle
-               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
+        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 
  ! r_buff_list is a read value for a buffer 
-               if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then
+             if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then
  ! Here the list is created
  ! Here the list is created
-                 ilist_sc=ilist_sc+1
+             ilist_sc=ilist_sc+1
  ! this can be substituted by cantor and anti-cantor
  ! this can be substituted by cantor and anti-cantor
-                 contlisti(ilist_sc)=i
-                 contlistj(ilist_sc)=j
+             contlisti(ilist_sc)=i
+             contlistj(ilist_sc)=j
  
  
-               endif
-             enddo
-             enddo
-             enddo
+             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,&
  !         call MPI_Reduce(ilist_sc,g_ilist_sc,1,&
  !          MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
  !        call MPI_Gather(newnss,1,MPI_INTEGER,&
@@ -27909,38 +27741,38 @@ chip1=chip(itypi)
  #endif
        if (nfgtasks.gt.1)then
  
  #endif
        if (nfgtasks.gt.1)then
  
-        call MPI_Reduce(ilist_sc,g_ilist_sc,1,&
-          MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
+      call MPI_Reduce(ilist_sc,g_ilist_sc,1,&
+        MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
  !        write(iout,*) "before bcast",g_ilist_sc
  !        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
+      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)        
  !        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)
+      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)
  !        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(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)
  
  
  !        call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
  
-        else
-        g_ilist_sc=ilist_sc
+      else
+      g_ilist_sc=ilist_sc
  
  
-        do i=1,ilist_sc
-        newcontlisti(i)=contlisti(i)
-        newcontlistj(i)=contlistj(i)
-        enddo
-        endif
+      do i=1,ilist_sc
+      newcontlisti(i)=contlisti(i)
+      newcontlistj(i)=contlistj(i)
+      enddo
+      endif
        
  #ifdef DEBUG
        write (iout,*) "after MPIREDUCE",g_ilist_sc
        
  #ifdef DEBUG
        write (iout,*) "after MPIREDUCE",g_ilist_sc
@@ -27948,7 +27780,7 @@ chip1=chip(itypi)
        write (iout,*) i,newcontlisti(i),newcontlistj(i)
        enddo
  #endif
        write (iout,*) i,newcontlisti(i),newcontlistj(i)
        enddo
  #endif
-        call int_bounds(g_ilist_sc,g_listscsc_start,g_listscsc_end)
+      call int_bounds(g_ilist_sc,g_listscsc_start,g_listscsc_end)
        return
        end subroutine make_SCSC_inter_list
  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
        return
        end subroutine make_SCSC_inter_list
  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@@ -27959,30 +27791,24 @@ chip1=chip(itypi)
        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
        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(200*nres),contlistscpj(200*nres)
+      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
  !      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
+          ilist_scp=0
        do i=iatscp_s,iatscp_e
        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))
-          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(i)
+      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
+      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
  ! Uncomment following three lines for SC-p interactions
  !         xj=c(1,nres+j)-xi
  !         yj=c(2,nres+j)-yi
@@ -27991,67 +27817,35 @@ chip1=chip(itypi)
  !          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
+        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
  #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
+            ! 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
  ! Here the list is created
-                 ilist_scp_first=ilist_scp_first+1
+             ilist_scp_first=ilist_scp_first+1
  ! this can be substituted by cantor and anti-cantor
  ! this can be substituted by cantor and anti-cantor
-                 contlistscpi_f(ilist_scp_first)=i
-                 contlistscpj_f(ilist_scp_first)=j
-              endif
+             contlistscpi_f(ilist_scp_first)=i
+             contlistscpj_f(ilist_scp_first)=j
+            endif
  #endif
  ! r_buff_list is a read value for a buffer 
  #endif
  ! r_buff_list is a read value for a buffer 
-               if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then
+             if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then
  ! Here the list is created
  ! Here the list is created
-                 ilist_scp=ilist_scp+1
+             ilist_scp=ilist_scp+1
  ! this can be substituted by cantor and anti-cantor
  ! this can be substituted by cantor and anti-cantor
-                 contlistscpi(ilist_scp)=i
-                 contlistscpj(ilist_scp)=j
-              endif
-             enddo
-             enddo
-             enddo
+             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
  #ifdef DEBUG
        write (iout,*) "before MPIREDUCE",ilist_scp
        do i=1,ilist_scp
@@ -28060,38 +27854,38 @@ chip1=chip(itypi)
  #endif
        if (nfgtasks.gt.1)then
  
  #endif
        if (nfgtasks.gt.1)then
  
-        call MPI_Reduce(ilist_scp,g_ilist_scp,1,&
-          MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
+      call MPI_Reduce(ilist_scp,g_ilist_scp,1,&
+        MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
  !        write(iout,*) "before bcast",g_ilist_sc
  !        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
+      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)
  !        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)
+      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)
  !        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(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)
  
  
  !        call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
  
-        else
-        g_ilist_scp=ilist_scp
+      else
+      g_ilist_scp=ilist_scp
  
  
-        do i=1,ilist_scp
-        newcontlistscpi(i)=contlistscpi(i)
-        newcontlistscpj(i)=contlistscpj(i)
-        enddo
-        endif
+      do i=1,ilist_scp
+      newcontlistscpi(i)=contlistscpi(i)
+      newcontlistscpj(i)=contlistscpj(i)
+      enddo
+      endif
  
  #ifdef DEBUG
        write (iout,*) "after MPIREDUCE",g_ilist_scp
  
  #ifdef DEBUG
        write (iout,*) "after MPIREDUCE",g_ilist_scp
@@ -28110,7 +27904,7 @@ chip1=chip(itypi)
  !  126  continue
  !      enddo
  #endif
  !  126  continue
  !      enddo
  #endif
-        call int_bounds(g_ilist_scp,g_listscp_start,g_listscp_end)
+      call int_bounds(g_ilist_scp,g_listscp_start,g_listscp_end)
  
        return
        end subroutine make_SCp_inter_list
  
        return
        end subroutine make_SCp_inter_list
@@ -28122,14 +27916,14 @@ chip1=chip(itypi)
        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
        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
+      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
        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(200*nres),contlistppj(200*nres)
+      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
  !      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
-!            print *,"START make_SC"
+!            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
              ilist_pp=0
        r_buff_list=5.0
        do i=iatel_s,iatel_e
@@ -28143,17 +27937,16 @@ chip1=chip(itypi)
          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
-             do j=ielstart(i),ielend(i)
+
+        call to_box(xmedi,ymedi,zmedi)
+        call lipid_layer(xmedi,ymedi,zmedi,sslipi,ssgradlipi)
  !          write (iout,*) i,j,itype(i,1),itype(j,1)
  !          write (iout,*) i,j,itype(i,1),itype(j,1)
-          if (itype(j,1).eq.ntyp1.or. itype(j+1,1).eq.ntyp1) cycle
+!          if (itype(j,1).eq.ntyp1.or. itype(j+1,1).eq.ntyp1) cycle
   
  ! 1,j)
   
  ! 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)
            dxj=dc(1,j)
            dyj=dc(2,j)
            dzj=dc(3,j)
@@ -28166,34 +27959,13 @@ chip1=chip(itypi)
            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
-
-      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
-          endif
-       enddo
-       enddo
-       enddo
-
+          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
        if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then
  ! Here the list is created
                   ilist_pp=ilist_pp+1
@@ -28201,9 +27973,9 @@ chip1=chip(itypi)
                   contlistppi(ilist_pp)=i
                   contlistppj(ilist_pp)=j
                endif
                   contlistppi(ilist_pp)=i
                   contlistppj(ilist_pp)=j
                endif
+!             enddo
               enddo
               enddo
               enddo
               enddo
-!             enddo
  #ifdef DEBUG
        write (iout,*) "before MPIREDUCE",ilist_pp
        do i=1,ilist_pp
  #ifdef DEBUG
        write (iout,*) "before MPIREDUCE",ilist_pp
        do i=1,ilist_pp