first changes for shielding

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

diff --git a/source/unres/src_MD-M/energy_p_new_barrier.F b/source/unres/src_MD-M/energy_p_new_barrier.F
index 2208b17..9d6982d 100644 (file)
--- a/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@ -137,6 +137,13 @@ c      print *,"Processor",myrank," computed USCSC"
 #ifdef TIMING
       time_vec=time_vec+MPI_Wtime()-time01
 #endif
+C Introduction of shielding effect first for each peptide group
+C the shielding factor is set this factor is describing how each
+C peptide group is shielded by side-chains
+C the matrix - shield_fac(i) the i index describe the ith between i and i+1
+      if (shield_mode.gt.0) then
+       call set_shield_fac
+      endif
 c      print *,"Processor",myrank," left VEC_AND_DERIV"
       if (ipot.lt.6) then
 #ifdef SPLITELE
@@ -3285,11 +3292,18 @@ C 14/01/2014 TURN3,TUNR4 does no go under periodic boundry condition
         if (i.le.1) cycle
 C        write(iout,*) "tu jest i",i
         if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+C changes suggested by Ana to avoid out of bounds
+     & .or.((i+4).gt.nres)
+     & .or.((i-1).le.0)
+C end of changes by Ana
      &  .or. itype(i+2).eq.ntyp1
-     &  .or. itype(i+3).eq.ntyp1
-     &  .or. itype(i-1).eq.ntyp1
-     &  .or. itype(i+4).eq.ntyp1
-     &  ) cycle
+     &  .or. itype(i+3).eq.ntyp1) cycle
+        if(i.gt.1)then
+          if(itype(i-1).eq.ntyp1)cycle
+        end if
+        if(i.LT.nres-3)then
+          if (itype(i+4).eq.ntyp1) cycle
+        end if
         dxi=dc(1,i)
         dyi=dc(2,i)
         dzi=dc(3,i)
@@ -3313,6 +3327,10 @@ C        write(iout,*) "tu jest i",i
       do i=iturn4_start,iturn4_end
         if (i.le.1) cycle
         if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+C changes suggested by Ana to avoid out of bounds
+     & .or.((i+5).gt.nres)
+     & .or.((i-1).le.0)
+C end of changes suggested by Ana
      &    .or. itype(i+3).eq.ntyp1
      &    .or. itype(i+4).eq.ntyp1
      &    .or. itype(i+5).eq.ntyp1
@@ -3377,6 +3395,10 @@ c
       do i=iatel_s,iatel_e
         if (i.le.1) cycle
         if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+C changes suggested by Ana to avoid out of bounds
+     & .or.((i+2).gt.nres)
+     & .or.((i-1).le.0)
+C end of changes by Ana
      &  .or. itype(i+2).eq.ntyp1
      &  .or. itype(i-1).eq.ntyp1
      &                ) cycle
@@ -3431,6 +3453,10 @@ c        write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
 C          write (iout,*) i,j
          if (j.le.1) cycle
           if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1
+C changes suggested by Ana to avoid out of bounds
+     & .or.((j+2).gt.nres)
+     & .or.((j-1).le.0)
+C end of changes by Ana
      & .or.itype(j+2).eq.ntyp1
      & .or.itype(j-1).eq.ntyp1
      &) cycle