From a5f7d9f55e6e0f07be66dce4c30740db41b6461e Mon Sep 17 00:00:00 2001 From: Adam Sieradzan Date: Fri, 26 Jun 2015 20:44:39 +0200 Subject: [PATCH] Changes suggested by Ana --- source/unres/src_MD-M/chainbuild.F | 25 +++++++++++++++++++++++++ source/unres/src_MD-M/energy_p_new_barrier.F | 16 ++++++++++++++++ 2 files changed, 41 insertions(+) diff --git a/source/unres/src_MD-M/chainbuild.F b/source/unres/src_MD-M/chainbuild.F index 3a1c47d..0721b72 100644 --- a/source/unres/src_MD-M/chainbuild.F +++ b/source/unres/src_MD-M/chainbuild.F @@ -411,11 +411,17 @@ c------------------------------------------ include 'COMMON.SETUP' include 'COMMON.MUCA' include 'COMMON.HAIRPIN' +C change suggested by Ana - begin + integer allareout +C change suggested by Ana - end j=1 chain_beg=1 C do i=1,nres C write(*,*) 'initial', i,j,c(j,i) C enddo +C change suggested by Ana - begin + allareout=1 +C change suggested by Ana -end do i=1,nres-1 if ((itype(i).eq.ntyp1).and.(itype(i+1).eq.ntyp1)) then chain_end=i @@ -426,6 +432,10 @@ C enddo c(j,k)=c(j,k)-ireturnval*boxxsize c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize enddo +C Suggested by Ana + if (chain_beg.eq.1) + & dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize +C Suggested by Ana -end endif chain_beg=i+1 allareout=1 @@ -486,6 +496,9 @@ C write(*,*) 'after no jump', i,j,c(j,i) C enddo C NOW Y dimension +C suggesed by Ana begins + allareout=1 +C suggested by Ana ends j=2 chain_beg=1 do i=1,nres-1 @@ -498,6 +511,10 @@ C NOW Y dimension c(j,k)=c(j,k)-ireturnval*boxysize c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize enddo +C Suggested by Ana + if (chain_beg.eq.1) + & dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize +C Suggested by Ana -end endif chain_beg=i+1 allareout=1 @@ -547,6 +564,10 @@ C NOW Y dimension c(j,i)=c(j,i)+nojumpval*boxysize c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize enddo +C Now Z dimension +C Suggested by Ana -begins + allareout=1 +C Suggested by Ana -ends j=3 chain_beg=1 do i=1,nres-1 @@ -559,6 +580,10 @@ C NOW Y dimension c(j,k)=c(j,k)-ireturnval*boxzsize c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize enddo +C Suggested by Ana + if (chain_beg.eq.1) + & dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize +C Suggested by Ana -end endif chain_beg=i+1 allareout=1 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 af14adb..d4465f6 100644 --- a/source/unres/src_MD-M/energy_p_new_barrier.F +++ b/source/unres/src_MD-M/energy_p_new_barrier.F @@ -3064,6 +3064,10 @@ C C 14/01/2014 TURN3,TUNR4 does no go under periodic boundry condition do i=iturn3_start,iturn3_end 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 @@ -3091,6 +3095,10 @@ C 14/01/2014 TURN3,TUNR4 does no go under periodic boundry condition enddo do i=iturn4_start,iturn4_end 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 @@ -3154,6 +3162,10 @@ c Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3 c do i=iatel_s,iatel_e 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 @@ -3207,6 +3219,10 @@ c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i) do j=ielstart(i),ielend(i) c write (iout,*) i,j,itype(i),itype(j) 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 -- 1.7.9.5