X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2FssMD.F;h=50e1040cfc5d1165a0236b8bf3d475e749d2479f;hb=b9025a366733ac0290debbd52ede3527d29c9ed5;hp=eab3c70a84da55cb9198635063875d220f3debd8;hpb=c6335222f02abf32e0cc697ec8a4666c754655b9;p=unres.git

diff --git a/source/unres/src_MD-M/ssMD.F b/source/unres/src_MD-M/ssMD.F
index eab3c70..50e1040 100644
--- a/source/unres/src_MD-M/ssMD.F
+++ b/source/unres/src_MD-M/ssMD.F
@@ -532,7 +532,7 @@ c     Local variables
      &     allihpb(maxdim),alljhpb(maxdim),
      &     newnss,newihpb(maxdim),newjhpb(maxdim)
       logical found
-      integer i_newnss(max_fg_procs),displ(max_fg_procs)
+      integer i_newnss(max_fg_procs),displ(0:max_fg_procs)
       integer g_newihpb(maxdim),g_newjhpb(maxdim),g_newnss
 
       allnss=0
@@ -1949,3 +1949,151 @@ c$$$      return
 c$$$      end                                                               
 c$$$
 c$$$C-----------------------------------------------------------------------------
+c$$$C-----------------------------------------------------------------------------
+         subroutine triple_ssbond_ene(resi,resj,resk,eij)
+      include 'DIMENSIONS'
+      include 'COMMON.SBRIDGE'
+      include 'COMMON.CHAIN'
+      include 'COMMON.DERIV'
+      include 'COMMON.LOCAL'
+      include 'COMMON.INTERACT'
+      include 'COMMON.VAR'
+      include 'COMMON.IOUNITS'
+      include 'COMMON.CALC'
+#ifndef CLUST
+#ifndef WHAM
+      include 'COMMON.MD'
+#endif
+#endif
+
+c     External functions
+      double precision h_base
+      external h_base
+
+c     Input arguments
+      integer resi,resj,resk
+
+c     Output arguments
+      double precision eij,eij1,eij2,eij3
+
+c     Local variables
+      logical havebond
+c      integer itypi,itypj,k,l
+      double precision rrij,ssd,deltat1,deltat2,deltat12,cosphi
+      double precision rrik,rrjk,rik,rjk,xi,xk,yi,yk,zi,zk,xij,yij,zij
+      double precision xik,yik,zik,xjk,yjk,zjk
+      double precision sig0ij,ljd,sig,fac,e1,e2
+      double precision dcosom1(3),dcosom2(3),ed
+      double precision pom1,pom2
+      double precision ljA,ljB,ljXs
+      double precision d_ljB(1:3)
+      double precision ssA,ssB,ssC,ssXs
+      double precision ssxm,ljxm,ssm,ljm
+      double precision d_ssxm(1:3),d_ljxm(1:3),d_ssm(1:3),d_ljm(1:3)
+
+      i=resi
+      j=resj
+      k=resk
+C      write(iout,*) resi,resj,resk
+      itypi=itype(i)
+      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)
+
+      itypj=itype(j)
+      xj=c(1,nres+j)
+      yj=c(2,nres+j)
+      zj=c(3,nres+j)
+      
+      dxj=dc_norm(1,nres+j)
+      dyj=dc_norm(2,nres+j)
+      dzj=dc_norm(3,nres+j)
+      dscj_inv=vbld_inv(j+nres)
+      itypk=itype(k)
+      xk=c(1,nres+k)
+      yk=c(2,nres+k)
+      zk=c(3,nres+k)
+      
+      dxk=dc_norm(1,nres+k)
+      dyk=dc_norm(2,nres+k)
+      dzk=dc_norm(3,nres+k)
+      dscj_inv=vbld_inv(k+nres)
+      xij=xj-xi
+      xik=xk-xi
+      xjk=xk-xj
+      yij=yj-yi
+      yik=yk-yi
+      yjk=yk-yj
+      zij=zj-zi
+      zik=zk-zi
+      zjk=zk-zj
+      rrij=(xij*xij+yij*yij+zij*zij)
+      rij=dsqrt(rrij)  ! sc_angular needs rij to really be the inverse
+      rrik=(xik*xik+yik*yik+zik*zik)
+      rik=dsqrt(rrik)
+      rrjk=(xjk*xjk+yjk*yjk+zjk*zjk)
+      rjk=dsqrt(rrjk)
+C there are three combination of distances for each trisulfide bonds
+C The first case the ith atom is the center
+C Energy function is E=d/(a*(x-y)**2+b*(x+y)**2+c) where x is first
+C distance y is second distance the a,b,c,d are parameters derived for
+C this problem d parameter was set as a penalty currenlty set to 1.
+      eij1=dtriss/(atriss*(rij-rik)**2+btriss*(rij+rik)**2+ctriss)
+C second case jth atom is center
+      eij2=dtriss/(atriss*(rij-rjk)**2+btriss*(rij+rjk)**2+ctriss)
+C the third case kth atom is the center
+      eij3=dtriss/(atriss*(rik-rjk)**2+btriss*(rik+rjk)**2+ctriss)
+C      eij2=0.0
+C      eij3=0.0
+C      eij1=0.0
+      eij=eij1+eij2+eij3
+C      write(iout,*)i,j,k,eij
+C The energy penalty calculated now time for the gradient part 
+C derivative over rij
+      fac=-eij1**2/dtriss*(2.0*atriss*(rij-rik)+2.0*btriss*(rij+rik))
+     &-eij2**2/dtriss*(2.0*atriss*(rij-rjk)+2.0*btriss*(rij+rjk))  
+            gg(1)=xij*fac/rij
+            gg(2)=yij*fac/rij
+            gg(3)=zij*fac/rij
+      do m=1,3
+        gvdwx(m,i)=gvdwx(m,i)-gg(m)
+        gvdwx(m,j)=gvdwx(m,j)+gg(m)
+      enddo
+      do l=1,3
+        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)+2.0*btriss*(rij+rik))
+     &-eij3**2/dtriss*(2.0*atriss*(rik-rjk)+2.0*btriss*(rik+rjk))
+            gg(1)=xik*fac/rik
+            gg(2)=yik*fac/rik
+            gg(3)=zik*fac/rik
+      do m=1,3
+        gvdwx(m,i)=gvdwx(m,i)-gg(m)
+        gvdwx(m,k)=gvdwx(m,k)+gg(m)
+      enddo
+      do l=1,3
+        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)+2.0*btriss*(rij+rjk))-
+     &eij3**2/dtriss*(-2.0*atriss*(rik-rjk)+2.0*btriss*(rik+rjk))
+            gg(1)=xjk*fac/rjk
+            gg(2)=yjk*fac/rjk
+            gg(3)=zjk*fac/rjk
+      do m=1,3
+        gvdwx(m,j)=gvdwx(m,j)-gg(m)
+        gvdwx(m,k)=gvdwx(m,k)+gg(m)
+      enddo
+      do l=1,3
+        gvdwc(l,j)=gvdwc(l,j)-gg(l)
+        gvdwc(l,k)=gvdwc(l,k)+gg(l)
+      enddo
+      return
+      end