X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;ds=sidebyside;f=source%2Funres%2Fsrc_MD%2Fenergy_p_new_barrier.F;h=156ef66b85ff3cb26f3b6c60f4f3d172289f613a;hb=f0bb9d6184e0ad0284b22456f057adbf414a3bdf;hp=391724576f7c3ee2dc21209a4559b50901d40fee;hpb=cc6bfed2a73175fb7329acdd60f3d89d9f25afbb;p=unres.git

diff --git a/source/unres/src_MD/energy_p_new_barrier.F b/source/unres/src_MD/energy_p_new_barrier.F
index 3917245..156ef66 100644
--- a/source/unres/src_MD/energy_p_new_barrier.F
+++ b/source/unres/src_MD/energy_p_new_barrier.F
@@ -131,6 +131,11 @@ C
 C Calculate electrostatic (H-bonding) energy of the main chain.
 C
   107 continue
+cmc
+cmc Sep-06: egb takes care of dynamic ss bonds too
+cmc
+      if (dyn_ss) call dyn_set_nss
+
 c      print *,"Processor",myrank," computed USCSC"
 #ifdef TIMING
 #ifdef MPI
@@ -774,7 +779,6 @@ c      enddo
         do i=1,4*nres
           glocbuf(i)=gloc(i,icg)
         enddo
-#define DEBUG
 #ifdef DEBUG
       write (iout,*) "gloc_sc before reduce"
       do i=1,nres
@@ -783,7 +787,6 @@ c      enddo
        enddo
       enddo
 #endif
-#undef DEBUG
         do i=1,nres
          do j=1,3
           gloc_scbuf(j,i)=gloc_sc(j,i,icg)
@@ -802,7 +805,6 @@ c      enddo
         call MPI_Reduce(gloc_scbuf(1,1),gloc_sc(1,1,icg),3*nres,
      &    MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
         time_reduce=time_reduce+MPI_Wtime()-time00
-#define DEBUG
 #ifdef DEBUG
       write (iout,*) "gloc_sc after reduce"
       do i=1,nres
@@ -811,7 +813,6 @@ c      enddo
        enddo
       enddo
 #endif
-#undef DEBUG
 #ifdef DEBUG
       write (iout,*) "gloc after reduce"
       do i=1,4*nres
@@ -1137,8 +1138,8 @@ C
 c      write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
       evdw=0.0D0
       do i=iatsc_s,iatsc_e
-        itypi=iabs(itype(i))
-        itypi1=iabs(itype(i+1))
+        itypi=itype(i)
+        itypi1=itype(i+1)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
@@ -1151,7 +1152,7 @@ C
 cd        write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
 cd   &                  'iend=',iend(i,iint)
           do j=istart(i,iint),iend(i,iint)
-            itypj=iabs(itype(j))
+            itypj=itype(j)
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
@@ -1314,8 +1315,8 @@ C
 c     print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
       evdw=0.0D0
       do i=iatsc_s,iatsc_e
-        itypi=iabs(itype(i))
-        itypi1=iabs(itype(i+1))
+        itypi=itype(i)
+        itypi1=itype(i+1)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
@@ -1324,7 +1325,7 @@ C Calculate SC interaction energy.
 C
         do iint=1,nint_gr(i)
           do j=istart(i,iint),iend(i,iint)
-            itypj=iabs(itype(j))
+            itypj=itype(j)
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
@@ -1431,8 +1432,8 @@ c     else
 c     endif
       ind=0
       do i=iatsc_s,iatsc_e
-        itypi=iabs(itype(i))
-        itypi1=iabs(itype(i+1))
+        itypi=itype(i)
+        itypi1=itype(i+1)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
@@ -1556,6 +1557,7 @@ C
       include 'COMMON.IOUNITS'
       include 'COMMON.CALC'
       include 'COMMON.CONTROL'
+      include 'COMMON.SBRIDGE'
       logical lprn
       evdw=0.0D0
 ccccc      energy_dec=.false.
@@ -1567,8 +1569,8 @@ c     print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
 c     if (icall.eq.0) lprn=.false.
       ind=0
       do i=iatsc_s,iatsc_e
-        itypi=iabs(itype(i))
-        itypi1=iabs(itype(i+1))
+        itypi=itype(i)
+        itypi1=itype(i+1)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
@@ -1584,8 +1586,12 @@ C Calculate SC interaction energy.
 C
         do iint=1,nint_gr(i)
           do j=istart(i,iint),iend(i,iint)
+            IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
+              call dyn_ssbond_ene(i,j,evdwij)
+              evdw=evdw+evdwij
+            ELSE
             ind=ind+1
-            itypj=iabs(itype(j))
+            itypj=itype(j)
 c            dscj_inv=dsc_inv(itypj)
             dscj_inv=vbld_inv(j+nres)
 c            write (iout,*) "j",j,dsc_inv(itypj),dscj_inv,
@@ -1693,6 +1699,7 @@ C Calculate angular part of the gradient.
 #else
             call sc_grad
 #endif
+            ENDIF    ! dyn_ss            
           enddo      ! j
         enddo        ! iint
       enddo          ! i
@@ -1726,8 +1733,8 @@ c     print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
 c     if (icall.eq.0) lprn=.true.
       ind=0
       do i=iatsc_s,iatsc_e
-        itypi=iabs(itype(i))
-        itypi1=iabs(itype(i+1))
+        itypi=itype(i)
+        itypi1=itype(i+1)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
@@ -1742,7 +1749,7 @@ C
         do iint=1,nint_gr(i)
           do j=istart(i,iint),iend(i,iint)
             ind=ind+1
-            itypj=iabs(itype(j))
+            itypj=itype(j)
 c            dscj_inv=dsc_inv(itypj)
             dscj_inv=vbld_inv(j+nres)
             sig0ij=sigma(itypi,itypj)
@@ -2046,8 +2053,8 @@ C
 cd    print *,'Entering Esoft_sphere nnt=',nnt,' nct=',nct
       evdw=0.0D0
       do i=iatsc_s,iatsc_e
-        itypi=iabs(itype(i))
-        itypi1=iabs(itype(i+1))
+        itypi=itype(i)
+        itypi1=itype(i+1)
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
@@ -2058,7 +2065,7 @@ C
 cd        write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
 cd   &                  'iend=',iend(i,iint)
           do j=istart(i,iint),iend(i,iint)
-            itypj=iabs(itype(j))
+            itypj=itype(j)
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
             zj=c(3,nres+j)-zi
@@ -4059,7 +4066,7 @@ cd    write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
         do iint=1,nscp_gr(i)
 
         do j=iscpstart(i,iint),iscpend(i,iint)
-          itypj=iabs(itype(j))
+          itypj=itype(j)
 C Uncomment following three lines for SC-p interactions
 c         xj=c(1,nres+j)-xi
 c         yj=c(2,nres+j)-yi
@@ -4153,7 +4160,7 @@ cd    write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
         do iint=1,nscp_gr(i)
 
         do j=iscpstart(i,iint),iscpend(i,iint)
-          itypj=iabs(itype(j))
+          itypj=itype(j)
 C Uncomment following three lines for SC-p interactions
 c         xj=c(1,nres+j)-xi
 c         yj=c(2,nres+j)-yi
@@ -4270,8 +4277,12 @@ c        write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj,
 c     &    dhpb(i),dhpb1(i),forcon(i)
 C 24/11/03 AL: SS bridges handled separately because of introducing a specific
 C    distance and angle dependent SS bond potential.
-        if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. iabs(itype(jjj
-     &)).eq.1) then
+cmc        if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+C 18/07/06 MC: Use the convention that the first nss pairs are SS bonds
+c          if (.not.dyn_ss .and. i.le.nss) then
+C 15/02/13 CC dynamic SSbond
+        if (.not.dyn_ss.and.
+     &   ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then 
           call ssbond_ene(iii,jjj,eij)
           ehpb=ehpb+2*eij
 cd          write (iout,*) "eij",eij
@@ -4375,7 +4386,7 @@ C
       include 'COMMON.VAR'
       include 'COMMON.IOUNITS'
       double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
-      itypi=iabs(itype(i))
+      itypi=itype(i)
       xi=c(1,nres+i)
       yi=c(2,nres+i)
       zi=c(3,nres+i)
@@ -4384,7 +4395,7 @@ C
       dzi=dc_norm(3,nres+i)
 c      dsci_inv=dsc_inv(itypi)
       dsci_inv=vbld_inv(nres+i)
-      itypj=iabs(itype(j))
+      itypj=itype(j)
 c      dscj_inv=dsc_inv(itypj)
       dscj_inv=vbld_inv(nres+j)
       xj=c(1,nres+j)-xi
@@ -4478,7 +4489,7 @@ c
 c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
 c
       do i=ibond_start,ibond_end
-        iti=iabs(itype(i))
+        iti=itype(i)
         if (iti.ne.10) then
           nbi=nbondterm(iti)
           if (nbi.eq.1) then
@@ -4553,7 +4564,7 @@ c     write (*,'(a,i2)') 'EBEND ICG=',icg
       do i=ithet_start,ithet_end
 C Zero the energy function and its derivative at 0 or pi.
         call splinthet(theta(i),0.5d0*delta,ss,ssd)
-        it=iabs(itype(i-1))
+        it=itype(i-1)
         if (i.gt.3) then
 #ifdef OSF
 	  phii=phi(i)
@@ -4767,7 +4778,7 @@ C
         dephii=0.0d0
         dephii1=0.0d0
         theti2=0.5d0*theta(i)
-        ityp2=ithetyp(iabs(itype(i-1)))
+        ityp2=ithetyp(itype(i-1))
         do k=1,nntheterm
           coskt(k)=dcos(k*theti2)
           sinkt(k)=dsin(k*theti2)
@@ -4779,7 +4790,7 @@ C
 #else
           phii=phi(i)
 #endif
-          ityp1=ithetyp(iabs(itype(i-2)))
+          ityp1=ithetyp(itype(i-2))
           do k=1,nsingle
             cosph1(k)=dcos(k*phii)
             sinph1(k)=dsin(k*phii)
@@ -4800,7 +4811,7 @@ C
 #else
           phii1=phi(i+1)
 #endif
-          ityp3=ithetyp(iabs(itype(i)))
+          ityp3=ithetyp(itype(i))
           do k=1,nsingle
             cosph2(k)=dcos(k*phii1)
             sinph2(k)=dsin(k*phii1)
@@ -4951,7 +4962,7 @@ c     write (iout,'(a)') 'ESC'
       do i=loc_start,loc_end
         it=itype(i)
         if (it.eq.10) goto 1
-        nlobit=nlob(iabs(it))
+        nlobit=nlob(it)
 c       print *,'i=',i,' it=',it,' nlobit=',nlobit
 c       write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
         theti=theta(i+1)-pipol
@@ -5108,11 +5119,11 @@ C Compute the contribution to SC energy and derivatives
 
           do j=1,nlobit
 #ifdef OSF
-            adexp=bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin
+            adexp=bsc(j,it)-0.5D0*contr(j,iii)+emin
             if(adexp.ne.adexp) adexp=1.0
             expfac=dexp(adexp)
 #else
-            expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin)
+            expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
 #endif
 cd          print *,'j=',j,' expfac=',expfac
             escloc_i=escloc_i+expfac
@@ -5194,7 +5205,7 @@ C Compute the contribution to SC energy and derivatives
 
       dersc12=0.0d0
       do j=1,nlobit
-        expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin)
+        expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
         escloc_i=escloc_i+expfac
         do k=1,2
           dersc(k)=dersc(k)+Ax(k,j)*expfac
@@ -8192,7 +8203,7 @@ c----------------------------------------------------------------------------
       include 'COMMON.GEO'
       logical swap
       double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
-     & auxvec1(2),auxvec2(1),auxmat1(2,2)
+     & auxvec1(2),auxvec2(2),auxmat1(2,2)
       logical lprn
       common /kutas/ lprn
 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC