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zmiany, wylaczenie diagnostyki, dzialajacy WHAM
author
Adam Kazimierz Sieradzan
<adasko@sun1.chem.univ.gda.pl>
Sun, 25 May 2014 15:23:08 +0000
(11:23 -0400)
committer
Adam Kazimierz Sieradzan
<adasko@sun1.chem.univ.gda.pl>
Sun, 25 May 2014 15:23:08 +0000
(11:23 -0400)
source/unres/src_MD-M/MREMD.F
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source/unres/src_MD-M/energy_p_new_barrier.F
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source/unres/src_MD-M/readpdb.F
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source/wham/src-M/energy_p_new.F
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diff --git
a/source/unres/src_MD-M/MREMD.F
b/source/unres/src_MD-M/MREMD.F
index
d9ddba2
..
df51b13
100644
(file)
--- 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
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)
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)
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)
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
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
enddo
nojumpval=0
do i=2,nres
@@
-1952,13
+1953,13
@@
C print *,'diff', difference
nojumpval=0
endif
endif
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
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
C NOW Y dimension
j=2
@@
-2002,8
+2003,8
@@
C NOW Y dimension
nojumpval=0
endif
endif
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
enddo
nojumpval=0
do i=2,nres
@@
-2019,8
+2020,8
@@
C NOW Y dimension
nojumpval=0
endif
endif
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
enddo
j=3
@@
-2064,8
+2065,8
@@
C NOW Y dimension
nojumpval=0
endif
endif
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
enddo
nojumpval=0
do i=2,nres
@@
-2081,8
+2082,8
@@
C NOW Y dimension
nojumpval=0
endif
endif
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
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
(file)
--- 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
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
& "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)
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
& "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
(file)
--- 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)
character*80 card
dimension sccor(3,20)
double precision e1(3),e2(3),e3(3)
- integer rescode
+ integer rescode,iterter(maxres)
logical fail
logical fail
+ do i=1,maxres
+ iterter(i)=0
+ enddo
ibeg=1
lsecondary=.false.
nhfrag=0
ibeg=1
lsecondary=.false.
nhfrag=0
@@
-48,7
+51,9
@@
crc----------------------------------------
C End current chain
ires_old=ires+2
itype(ires_old-1)=ntyp1
C End current chain
ires_old=ires+2
itype(ires_old-1)=ntyp1
+ iterter(ires_old-1)=1
itype(ires_old)=ntyp1
itype(ires_old)=ntyp1
+ iterter(ires_old)=1
ibeg=2
write (iout,*) "Chain ended",ires,ishift,ires_old
if (unres_pdb) then
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)
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
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
(file)
--- 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
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
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)
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)
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
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
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
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,
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
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
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
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)
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)
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
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)
estr=estr+uprod/usum
do j=1,3
gradbx(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres)