From: Adam Kazimierz Sieradzan Date: Sun, 25 May 2014 15:23:08 +0000 (-0400) Subject: zmiany, wylaczenie diagnostyki, dzialajacy WHAM X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=1e3c2bda475e5d4031b8dab868bb8bf379a9e388 zmiany, wylaczenie diagnostyki, dzialajacy WHAM --- diff --git a/source/unres/src_MD-M/MREMD.F b/source/unres/src_MD-M/MREMD.F index d9ddba2..df51b13 100644 --- a/source/unres/src_MD-M/MREMD.F +++ b/source/unres/src_MD-M/MREMD.F @@ -527,6 +527,7 @@ c Variable time step algorithm. enddo C print *,'przed returnbox' call returnbox +C call enerprint(remd_ene(0,i)) do i=1,nres*2 do j=1,3 c_cache(j,i,ntwx_cache)=c(j,i) @@ -832,7 +833,7 @@ c & remd_t_bath(iex) call rescale_weights(remd_t_bath(iex)) c write (iout,*) "0,i",remd_t_bath(iex) -c call enerprint(remd_ene(0,i)) + call enerprint(remd_ene(0,i)) call sum_energy(remd_ene(0,i),.false.) c write (iout,*) "ene_i_iex",remd_ene(0,i) @@ -1935,8 +1936,8 @@ C print *,'diff', difference nojumpval=0 endif endif - c(j,k)=c(j,k)+nojumpval*boxxsize - c(j,k+nres)=c(j,k+nres)+nojumpval*boxxsize + c(j,i)=c(j,i)+nojumpval*boxxsize + c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize enddo nojumpval=0 do i=2,nres @@ -1952,13 +1953,13 @@ C print *,'diff', difference nojumpval=0 endif endif - c(j,k)=c(j,k)+nojumpval*boxxsize - c(j,k+nres)=c(j,k+nres)+nojumpval*boxxsize + c(j,i)=c(j,i)+nojumpval*boxxsize + c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize enddo - do i=1,nres - write(*,*) 'after no jump', i,j,c(j,i) - enddo +C do i=1,nres +C write(*,*) 'after no jump', i,j,c(j,i) +C enddo C NOW Y dimension j=2 @@ -2002,8 +2003,8 @@ C NOW Y dimension nojumpval=0 endif endif - c(j,k)=c(j,k)+nojumpval*boxysize - c(j,k+nres)=c(j,k+nres)+nojumpval*boxysize + c(j,i)=c(j,i)+nojumpval*boxysize + c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize enddo nojumpval=0 do i=2,nres @@ -2019,8 +2020,8 @@ C NOW Y dimension nojumpval=0 endif endif - c(j,k)=c(j,k)+nojumpval*boxysize - c(j,k+nres)=c(j,k+nres)+nojumpval*boxysize + c(j,i)=c(j,i)+nojumpval*boxysize + c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize enddo j=3 @@ -2064,8 +2065,8 @@ C NOW Y dimension nojumpval=0 endif endif - c(j,k)=c(j,k)+nojumpval*boxzsize - c(j,k+nres)=c(j,k+nres)+nojumpval*boxzsize + c(j,i)=c(j,i)+nojumpval*boxzsize + c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize enddo nojumpval=0 do i=2,nres @@ -2081,8 +2082,8 @@ C NOW Y dimension nojumpval=0 endif endif - c(j,k)=c(j,k)+nojumpval*boxzsize - c(j,k+nres)=c(j,k+nres)+nojumpval*boxzsize + c(j,i)=c(j,i)+nojumpval*boxzsize + c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize enddo return 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 c8acad2..23aafae 100644 --- a/source/unres/src_MD-M/energy_p_new_barrier.F +++ b/source/unres/src_MD-M/energy_p_new_barrier.F @@ -4787,7 +4787,7 @@ C YES vbldpDUM is the equlibrium length of spring for Dummy atom C NO vbldp0 is the equlibrium lenght of spring for peptide group diff = vbld(i)-vbldp0 endif - if (energy_dec) write (iout,'(a7,i5,4f7.3)') + if (energy_dec) write (iout,'(a7,i5,4f7.3)') & "estr bb",i,vbld(i),vbldp0,diff,AKP*diff*diff estr=estr+diff*diff do j=1,3 @@ -4806,7 +4806,7 @@ c nbi=nbondterm(iti) if (nbi.eq.1) then diff=vbld(i+nres)-vbldsc0(1,iti) - if (energy_dec) write (iout,*) + if (energy_dec) write (iout,*) & "estr sc",i,iti,vbld(i+nres),vbldsc0(1,iti),diff, & AKSC(1,iti),AKSC(1,iti)*diff*diff estr=estr+0.5d0*AKSC(1,iti)*diff*diff diff --git a/source/unres/src_MD-M/readpdb.F b/source/unres/src_MD-M/readpdb.F index ca0be94..978d0ae 100644 --- a/source/unres/src_MD-M/readpdb.F +++ b/source/unres/src_MD-M/readpdb.F @@ -17,8 +17,11 @@ C geometry. character*80 card dimension sccor(3,20) double precision e1(3),e2(3),e3(3) - integer rescode + integer rescode,iterter(maxres) logical fail + do i=1,maxres + iterter(i)=0 + enddo ibeg=1 lsecondary=.false. nhfrag=0 @@ -48,7 +51,9 @@ crc---------------------------------------- C End current chain ires_old=ires+2 itype(ires_old-1)=ntyp1 + iterter(ires_old-1)=1 itype(ires_old)=ntyp1 + iterter(ires_old)=1 ibeg=2 write (iout,*) "Chain ended",ires,ishift,ires_old if (unres_pdb) then @@ -120,8 +125,8 @@ C system nres=ires do i=2,nres-1 write (iout,*) i,itype(i),itype(i+1) - if (itype(i).eq.ntyp1) then - if (itype(i+1).eq.ntyp1) then + if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then + if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then C 16/01/2014 by Adasko: Adding to dummy atoms in the chain C first is connected prevous chain (itype(i+1).eq.ntyp1)=true C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false diff --git a/source/wham/src-M/energy_p_new.F b/source/wham/src-M/energy_p_new.F index 810275a..7217542 100644 --- a/source/wham/src-M/energy_p_new.F +++ b/source/wham/src-M/energy_p_new.F @@ -1908,11 +1908,15 @@ C write (iout,*) 'iatel_s=',iatel_s,' iatel_e=',iatel_e gcorr_loc(i)=0.0d0 enddo do i=iatel_s,iatel_e - if (i.eq.1) cycle + if (i.eq.1) then + if (itype(i).eq.ntyp1.or. itype(i+1).eq.ntyp1 + & .or. itype(i+2).eq.ntyp1) cycle + else if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 & .or. itype(i+2).eq.ntyp1 & .or. itype(i-1).eq.ntyp1 &) cycle + endif if (itel(i).eq.0) goto 1215 dxi=dc(1,i) dyi=dc(2,i) @@ -1932,11 +1936,16 @@ C write (iout,*) 'iatel_s=',iatel_s,' iatel_e=',iatel_e num_conti=0 C write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i) do j=ielstart(i),ielend(i) - if (j.eq.1) cycle + if (j.eq.1) then + if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1 + & .or.itype(j+2).eq.ntyp1 + &) cycle + else if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1 & .or.itype(j+2).eq.ntyp1 & .or.itype(j-1).eq.ntyp1 &) cycle + endif C C) cycle if (itel(j).eq.0) goto 1216 @@ -2032,7 +2041,7 @@ c write (iout,'(a6,2i5,0pf7.3,2i5,2e11.3)') c &'evdw1',i,j,evdwij c &,iteli,itelj,aaa,evdw1 - write (iout,'(a6,2i5,0pf7.3)') 'ees',i,j,eesij +C write (iout,'(a6,2i5,0pf7.3)') 'ees',i,j,eesij c write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)') c & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i, c & 1.0D0/dsqrt(rrmij),evdwij,eesij, @@ -3272,13 +3281,14 @@ C else else diff = vbld(i)-vbldp0 c write (iout,*) i,vbld(i),vbldp0,diff,AKP*diff*diff + endif estr=estr+diff*diff do j=1,3 gradb(j,i-1)=AKP*diff*dc(j,i-1)/vbld(i) enddo - endif - write (iout,'(a7,i5,4f7.3)') - & "estr bb",i,vbld(i),vbldp0,diff,AKP*diff*diff +C endif +C write (iout,'(a7,i5,4f7.3)') +C & "estr bb",i,vbld(i),vbldp0,diff,AKP*diff*diff enddo estr=0.5d0*AKP*estr+estr1 c @@ -3290,8 +3300,8 @@ c nbi=nbondterm(iti) if (nbi.eq.1) then diff=vbld(i+nres)-vbldsc0(1,iti) -c write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff, -c & AKSC(1,iti),AKSC(1,iti)*diff*diff +C write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff, +C & AKSC(1,iti),AKSC(1,iti)*diff*diff estr=estr+0.5d0*AKSC(1,iti)*diff*diff do j=1,3 gradbx(j,i)=AKSC(1,iti)*diff*dc(j,i+nres)/vbld(i+nres) @@ -3320,8 +3330,8 @@ c & AKSC(1,iti),AKSC(1,iti)*diff*diff usum=usum+uprod1 usumsqder=usumsqder+ud(j)*uprod2 enddo -c write (iout,*) i,iti,vbld(i+nres),(vbldsc0(j,iti), -c & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi) + write (iout,*) i,iti,vbld(i+nres),(vbldsc0(j,iti), + & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi) estr=estr+uprod/usum do j=1,3 gradbx(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres)