readpdb correction

[unres.git] / source / unres / src_MD-M / ssMD.F

diff --git a/source/unres/src_MD-M/ssMD.F b/source/unres/src_MD-M/ssMD.F
index 8b7f2a4..51ad513 100644 (file)
--- a/source/unres/src_MD-M/ssMD.F
+++ b/source/unres/src_MD-M/ssMD.F
@@ -655,38 +655,7 @@ c     &       "SSBOND_FORM",totT,t_bath,newihpb(i),newjhpb(i)
       return
       end
 
-c----------------------------------------------------------------------------
-
-#ifdef WHAM
-      subroutine read_ssHist
-      implicit none
-
-c     Includes
-      include 'DIMENSIONS'
-      include "DIMENSIONS.FREE"
-      include 'COMMON.FREE'
-
-c     Local variables
-      integer i,j
-      character*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))
-      enddo
-
-      return
-      end
-#endif
 
-c----------------------------------------------------------------------------
-
-
-C-----------------------------------------------------------------------------
-C-----------------------------------------------------------------------------
-C-----------------------------------------------------------------------------
-C-----------------------------------------------------------------------------
 C-----------------------------------------------------------------------------
 C-----------------------------------------------------------------------------
 C-----------------------------------------------------------------------------
@@ -1990,6 +1959,7 @@ c      integer itypi,itypj,k,l
       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)
+      eij=0.0
       if (dtriss.eq.0) return
       i=resi
       j=resj
@@ -2042,11 +2012,23 @@ 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)
+      if ((iabs(j-i).le.2).or.(iabs(i-k).le.2)) then
+      eij1=0.0d0
+      else
+      eij1=dtriss/(atriss*(rij-rik)**2+btriss*(rij+rik)**6+ctriss)
+      endif
 C second case jth atom is center
-      eij2=dtriss/(atriss*(rij-rjk)**2+btriss*(rij+rjk)**2+ctriss)
+      if ((iabs(j-i).le.2).or.(iabs(j-k).le.2)) then
+      eij2=0.0d0
+      else
+      eij2=dtriss/(atriss*(rij-rjk)**2+btriss*(rij+rjk)**6+ctriss)
+      endif
 C the third case kth atom is the center
-      eij3=dtriss/(atriss*(rik-rjk)**2+btriss*(rik+rjk)**2+ctriss)
+      if ((iabs(i-k).le.2).or.(iabs(j-k).le.2)) then
+      eij3=0.0d0
+      else
+      eij3=dtriss/(atriss*(rik-rjk)**2+btriss*(rik+rjk)**6+ctriss)
+      endif
 C      eij2=0.0
 C      eij3=0.0
 C      eij1=0.0
@@ -2054,8 +2036,8 @@ C      eij1=0.0
 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))  
+      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
@@ -2068,8 +2050,9 @@ C derivative over rij
         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))
+      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
@@ -2082,8 +2065,9 @@ C now derivative over rik
         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))
+      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