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Corrected WHAM and UNRES reading in SS dyn...
author
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Sun, 24 May 2015 12:46:48 +0000
(14:46 +0200)
committer
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Sun, 24 May 2015 12:46:48 +0000
(14:46 +0200)
source/unres/src_MD-M/parmread.F
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source/wham/src-M/geomout.F
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source/wham/src-M/include_unres/COMMON.SBRIDGE
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source/wham/src-M/parmread.F
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source/wham/src-M/ssMD.F
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diff --git
a/source/unres/src_MD-M/parmread.F
b/source/unres/src_MD-M/parmread.F
index
3296e45
..
c841df2
100644
(file)
--- a/
source/unres/src_MD-M/parmread.F
+++ b/
source/unres/src_MD-M/parmread.F
@@
-1256,7
+1256,7
@@
c lprint=.false.
C
C Define the constants of the disulfide bridge
C
C
C Define the constants of the disulfide bridge
C
- ebr=-12.00D0
+C ebr=-12.00D0
c
c Old arbitrary potential - commented out.
c
c
c Old arbitrary potential - commented out.
c
diff --git
a/source/wham/src-M/geomout.F
b/source/wham/src-M/geomout.F
index
c9110ae
..
6747e76
100644
(file)
--- a/
source/wham/src-M/geomout.F
+++ b/
source/wham/src-M/geomout.F
@@
-54,11
+54,11
@@
write (ipdb,30) ica(nct),ica(nct)+1
endif
do i=1,nss
write (ipdb,30) ica(nct),ica(nct)+1
endif
do i=1,nss
- if (dyn_ss) then
- write (iunit,30) ica(idssb(i))+1,ica(jdssb(i))+1
- else
- write (ipdb,30) ica(ihpb(i)-nres)+1,ica(jhpb(i)-nres)+1
- endif
+C if (dyn_ss) then
+C write (iunit,30) ica(idssb(i))+1,ica(jdssb(i))+1
+C else
+C write (ipdb,30) ica(ihpb(i)-nres)+1,ica(jhpb(i)-nres)+1
+C endif
enddo
write (ipdb,'(a6)') 'ENDMDL'
10 FORMAT ('ATOM',I7,' CA ',A3,1X,A1,I4,4X,3F8.3,f15.3)
enddo
write (ipdb,'(a6)') 'ENDMDL'
10 FORMAT ('ATOM',I7,' CA ',A3,1X,A1,I4,4X,3F8.3,f15.3)
diff --git
a/source/wham/src-M/include_unres/COMMON.SBRIDGE
b/source/wham/src-M/include_unres/COMMON.SBRIDGE
index
144a864
..
1380548
100644
(file)
--- a/
source/wham/src-M/include_unres/COMMON.SBRIDGE
+++ b/
source/wham/src-M/include_unres/COMMON.SBRIDGE
@@
-12,7
+12,7
@@
common /links_split/ link_start,link_end
double precision Ht,dyn_ssbond_ij,dtriss,atriss,btriss,ctriss
logical dyn_ss,dyn_ss_mask
common /links_split/ link_start,link_end
double precision Ht,dyn_ssbond_ij,dtriss,atriss,btriss,ctriss
logical dyn_ss,dyn_ss_mask
- common /dyn_ssbond/ dtriss,atriss,btriss,ctriss,
+ common /dyn_ssbond/ dtriss,atriss,btriss,ctriss,Ht,
& dyn_ssbond_ij(maxres,maxres),
& idssb(maxdim),jdssb(maxdim),
& dyn_ssbond_ij(maxres,maxres),
& idssb(maxdim),jdssb(maxdim),
- & Ht,dyn_ss,dyn_ss_mask(maxres)
+ & dyn_ss,dyn_ss_mask(maxres)
diff --git
a/source/wham/src-M/parmread.F
b/source/wham/src-M/parmread.F
index
d50cd03
..
750f03e
100644
(file)
--- a/
source/wham/src-M/parmread.F
+++ b/
source/wham/src-M/parmread.F
@@
-35,6
+35,7
@@
C
character*16 key
integer iparm
double precision ip,mp
character*16 key
integer iparm
double precision ip,mp
+C write (iout,*) "KURWA"
C
C Body
C
C
C Body
C
@@
-55,6
+56,14
@@
C Assign virtual-bond length
write (iout,*) "iparm",iparm," myparm",myparm
c If reading not own parameters, skip assignment
write (iout,*) "iparm",iparm," myparm",myparm
c If reading not own parameters, skip assignment
+ call reada(weightcard,"D0CM",d0cm,3.78d0)
+ call reada(weightcard,"AKCM",akcm,15.1d0)
+ call reada(weightcard,"AKTH",akth,11.0d0)
+ call reada(weightcard,"AKCT",akct,12.0d0)
+ call reada(weightcard,"V1SS",v1ss,-1.08d0)
+ call reada(weightcard,"V2SS",v2ss,7.61d0)
+ call reada(weightcard,"V3SS",v3ss,13.7d0)
+ call reada(weightcard,"EBR",ebr,-5.50D0)
call reada(controlcard,"DTRISS",dtriss,1.0D0)
call reada(controlcard,"ATRISS",atriss,0.3D0)
call reada(controlcard,"BTRISS",btriss,0.02D0)
call reada(controlcard,"DTRISS",dtriss,1.0D0)
call reada(controlcard,"ATRISS",atriss,0.3D0)
call reada(controlcard,"BTRISS",btriss,0.02D0)
@@
-63,24
+72,45
@@
c If reading not own parameters, skip assignment
C do i=1,maxres
C dyn_ss_mask(i)=.false.
C enddo
C do i=1,maxres
C dyn_ss_mask(i)=.false.
C enddo
+C ebr=-12.0D0
+c
+c Old arbitrary potential - commented out.
+c
+c dbr= 4.20D0
+c fbr= 3.30D0
+c
+c Constants of the disulfide-bond potential determined based on the RHF/6-31G**
+c energy surface of diethyl disulfide.
+c A. Liwo and U. Kozlowska, 11/24/03
+c
+ D0CM = 3.78d0
+ AKCM = 15.1d0
+ AKTH = 11.0d0
+ AKCT = 12.0d0
+ V1SS =-1.08d0
+ V2SS = 7.61d0
+ V3SS = 13.7d0
+
do i=1,maxres-1
do j=i+1,maxres
dyn_ssbond_ij(i,j)=1.0d300
enddo
enddo
call reada(controlcard,"HT",Ht,0.0D0)
do i=1,maxres-1
do j=i+1,maxres
dyn_ssbond_ij(i,j)=1.0d300
enddo
enddo
call reada(controlcard,"HT",Ht,0.0D0)
- if (dyn_ss) then
- ss_depth=ebr/wsc-0.25*eps(1,1)
- Ht=Ht/wsc-0.25*eps(1,1)
- akcm=akcm*wstrain/wsc
- akth=akth*wstrain/wsc
- akct=akct*wstrain/wsc
- v1ss=v1ss*wstrain/wsc
- v2ss=v2ss*wstrain/wsc
- v3ss=v3ss*wstrain/wsc
- else
- ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
- endif
+C if (dyn_ss) then
+C ss_depth=ebr/wsc-0.25*eps(1,1)
+C write(iout,*) HT,wsc,eps(1,1),'KURWA'
+C Ht=Ht/wsc-0.25*eps(1,1)
+
+C akcm=akcm*whpb/wsc
+C akth=akth*whpb/wsc
+C akct=akct*whpb/wsc
+C v1ss=v1ss*whpb/wsc
+C v2ss=v2ss*whpb/wsc
+C v3ss=v3ss*whpb/wsc
+C else
+C ss_depth=ebr/whpb-0.25*eps(1,1)*wsc/whpb
+C endif
if (iparm.eq.myparm .or. .not.separate_parset) then
if (iparm.eq.myparm .or. .not.separate_parset) then
@@
-104,7
+134,7
@@
c
wvdwpp=ww(16)
wbond=ww(18)
wsccor=ww(19)
wvdwpp=ww(16)
wbond=ww(18)
wsccor=ww(19)
-
+ whpb=ww(15)
endif
call card_concat(controlcard,.false.)
endif
call card_concat(controlcard,.false.)
@@
-1217,7
+1247,7
@@
C
C
C Define the constants of the disulfide bridge
C
C
C Define the constants of the disulfide bridge
C
- ebr=-5.50D0
+C ebr=-12.0D0
c
c Old arbitrary potential - commented out.
c
c
c Old arbitrary potential - commented out.
c
@@
-1228,21
+1258,36
@@
c Constants of the disulfide-bond potential determined based on the RHF/6-31G**
c energy surface of diethyl disulfide.
c A. Liwo and U. Kozlowska, 11/24/03
c
c energy surface of diethyl disulfide.
c A. Liwo and U. Kozlowska, 11/24/03
c
- D0CM = 3.78d0
- AKCM = 15.1d0
- AKTH = 11.0d0
- AKCT = 12.0d0
- V1SS =-1.08d0
- V2SS = 7.61d0
- V3SS = 13.7d0
+C D0CM = 3.78d0
+C AKCM = 15.1d0
+C AKTH = 11.0d0
+C AKCT = 12.0d0
+C V1SS =-1.08d0
+C V2SS = 7.61d0
+C V3SS = 13.7d0
- if (lprint) then
+ if (dyn_ss) then
+ ss_depth=ebr/wsc-0.25*eps(1,1)
+C write(iout,*) akcm,whpb,wsc,'KURWA'
+ Ht=Ht/wsc-0.25*eps(1,1)
+
+ akcm=akcm*whpb/wsc
+ akth=akth*whpb/wsc
+ akct=akct*whpb/wsc
+ v1ss=v1ss*whpb/wsc
+ v2ss=v2ss*whpb/wsc
+ v3ss=v3ss*whpb/wsc
+ else
+ ss_depth=ebr/whpb-0.25*eps(1,1)*wsc/whpb
+ endif
+
+C if (lprint) then
write (iout,'(/a)') "Disulfide bridge parameters:"
write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,
& ' v3ss:',v3ss
write (iout,'(/a)') "Disulfide bridge parameters:"
write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,
& ' v3ss:',v3ss
- endif
+C endif
return
end
return
end
diff --git
a/source/wham/src-M/ssMD.F
b/source/wham/src-M/ssMD.F
index
283adf3
..
5080b18
100644
(file)
--- a/
source/wham/src-M/ssMD.F
+++ b/
source/wham/src-M/ssMD.F
@@
-251,6
+251,7
@@
c-------END TESTING CODE
e1=fac*fac*aa(itypi,itypj)
e2=fac*bb(itypi,itypj)
eij=eps1*eps2rt*eps3rt*(e1+e2)
e1=fac*fac*aa(itypi,itypj)
e2=fac*bb(itypi,itypj)
eij=eps1*eps2rt*eps3rt*(e1+e2)
+C write(iout,*) eij,'TU?1'
eps2der=eij*eps3rt
eps3der=eij*eps2rt
eij=eij*eps2rt*eps3rt
eps2der=eij*eps3rt
eps3der=eij*eps2rt
eij=eij*eps2rt*eps3rt
@@
-267,7
+268,7
@@
c-------END TESTING CODE
havebond=.true.
ssd=rij-ssXs
eij=ssA*ssd*ssd+ssB*ssd+ssC
havebond=.true.
ssd=rij-ssXs
eij=ssA*ssd*ssd+ssB*ssd+ssC
-
+C write(iout,*) 'TU?2',ssc,ssd
ed=2*akcm*ssd+akct*deltat12
pom1=akct*ssd
pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi
ed=2*akcm*ssd+akct*deltat12
pom1=akct*ssd
pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi
@@
-303,6
+304,7
@@
c-------FIRST METHOD, DISCONTINUOUS SECOND DERIVATIVE
h1=h_base(f1,hd1)
h2=h_base(f2,hd2)
eij=ssm*h1+Ht*h2
h1=h_base(f1,hd1)
h2=h_base(f2,hd2)
eij=ssm*h1+Ht*h2
+C write(iout,*) eij,'TU?3'
delta_inv=1.0d0/(xm-ssxm)
deltasq_inv=delta_inv*delta_inv
fac=ssm*hd1-Ht*hd2
delta_inv=1.0d0/(xm-ssxm)
deltasq_inv=delta_inv*delta_inv
fac=ssm*hd1-Ht*hd2
@@
-325,6
+327,7
@@
c-------FIRST METHOD, DISCONTINUOUS SECOND DERIVATIVE
h1=h_base(f1,hd1)
h2=h_base(f2,hd2)
eij=Ht*h1+ljm*h2
h1=h_base(f1,hd1)
h2=h_base(f2,hd2)
eij=Ht*h1+ljm*h2
+C write(iout,*) 'TU?4',ssA
delta_inv=1.0d0/(ljxm-xm)
deltasq_inv=delta_inv*delta_inv
fac=Ht*hd1-ljm*hd2
delta_inv=1.0d0/(ljxm-xm)
deltasq_inv=delta_inv*delta_inv
fac=Ht*hd1-ljm*hd2
@@
-396,7
+399,7
@@
c$$$ if (ed.gt.0.0d0) havebond=.true.
c-------END SECOND METHOD, CONTINUOUS SECOND DERIVATIVE
endif
c-------END SECOND METHOD, CONTINUOUS SECOND DERIVATIVE
endif
-
+ write(iout,*) 'havebond',havebond
if (havebond) then
#ifndef CLUST
#ifndef WHAM
if (havebond) then
#ifndef CLUST
#ifndef WHAM