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poprawka turn3 i turn4 uwaga moga byc wlaczone diagnostki
author
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Mon, 23 Feb 2015 19:00:58 +0000
(20:00 +0100)
committer
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Mon, 23 Feb 2015 19:00:58 +0000
(20:00 +0100)
source/unres/src_MD/COMMON.DERIV
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source/unres/src_MD/COMMON.SCCOR
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source/unres/src_MD/checkder_p.F
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source/unres/src_MD/energy_p_new_barrier.F
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source/unres/src_MD/intcartderiv.F
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source/unres/src_MD/unres.F
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diff --git
a/source/unres/src_MD/COMMON.DERIV
b/source/unres/src_MD/COMMON.DERIV
index
6fdb1aa
..
e4c39c5
100644
(file)
--- a/
source/unres/src_MD/COMMON.DERIV
+++ b/
source/unres/src_MD/COMMON.DERIV
@@
-2,7
+2,9
@@
& gvdwpp,gel_loc,gel_loc_long,gvdwc_scpp,
& gradx_scp,gvdwc_scp,ghpbx,ghpbc,gloc,gloc_x,dtheta,dphi,dalpha,
& domega,gscloc,gsclocx,gradcorr,gradcorr_long,gradcorr5_long,
& gvdwpp,gel_loc,gel_loc_long,gvdwc_scpp,
& gradx_scp,gvdwc_scp,ghpbx,ghpbc,gloc,gloc_x,dtheta,dphi,dalpha,
& domega,gscloc,gsclocx,gradcorr,gradcorr_long,gradcorr5_long,
- & gradcorr6_long,gcorr6_turn_long,gvdwcT,gvdwxT,gvdwx
+ & gradcorr6_long,gcorr6_turn_long,gvdwcT,gvdwxT,gvdwx,gloc_sc,
+ & dcostau,dsintau,dtauangle,dcosomicron,
+ & domicron
integer nfl,icg
common /derivatT/ gvdwcT(3,maxres),gvdwxT(3,maxres)
common /derivat/ dcdv(6,maxdim),dxdv(6,maxdim),dxds(6,maxres),
integer nfl,icg
common /derivatT/ gvdwcT(3,maxres),gvdwxT(3,maxres)
common /derivat/ dcdv(6,maxdim),dxdv(6,maxdim),dxds(6,maxres),
@@
-21,7
+23,10
@@
& gel_loc_turn4(maxvar),gel_loc_turn6(maxvar),gcorr_loc(maxvar),
& g_corr5_loc(maxvar),g_corr6_loc(maxvar),gsccorc(3,maxres),
& gsccorx(3,maxres),gsccor_loc(maxres),dtheta(3,2,maxres),
& gel_loc_turn4(maxvar),gel_loc_turn6(maxvar),gcorr_loc(maxvar),
& g_corr5_loc(maxvar),g_corr6_loc(maxvar),gsccorc(3,maxres),
& gsccorx(3,maxres),gsccor_loc(maxres),dtheta(3,2,maxres),
- & gscloc(3,maxres),gsclocx(3,maxres),
+ & gscloc(3,maxres),gsclocx(3,maxres),gloc_sc(3,0:maxres2,10),
+ & dcostau(3,3,3,maxres2),dsintau(3,3,3,maxres2),
+ & dtauangle(3,3,3,maxres2),dcosomicron(3,3,3,maxres2),
+ & domicron(3,3,3,maxres2),
& dphi(3,3,maxres),dalpha(3,3,maxres),domega(3,3,maxres),nfl,icg
double precision derx,derx_turn
common /deriv_loc/ derx(3,5,2),derx_turn(3,5,2)
& dphi(3,3,maxres),dalpha(3,3,maxres),domega(3,3,maxres),nfl,icg
double precision derx,derx_turn
common /deriv_loc/ derx(3,5,2),derx_turn(3,5,2)
diff --git
a/source/unres/src_MD/COMMON.SCCOR
b/source/unres/src_MD/COMMON.SCCOR
index
208d60b
..
623bbad
100644
(file)
--- a/
source/unres/src_MD/COMMON.SCCOR
+++ b/
source/unres/src_MD/COMMON.SCCOR
@@
-1,18
+1,20
@@
cc Parameters of the SCCOR term
double precision v1sccor,v2sccor,vlor1sccor,
cc Parameters of the SCCOR term
double precision v1sccor,v2sccor,vlor1sccor,
- & vlor2sccor,vlor3sccor,gloc_sc,
- & dcostau,dsintau,dtauangle,dcosomicron,
- & domicron,v0sccor
+ & vlor2sccor,vlor3sccor,v0sccor
+C,gloc_sc,
+C & dcostau,dsintau,dtauangle,dcosomicron,
+C & domicron,v0sccor
integer nterm_sccor,isccortyp,nsccortyp,nlor_sccor
common/sccor/v1sccor(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp),
& v2sccor(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp),
integer nterm_sccor,isccortyp,nsccortyp,nlor_sccor
common/sccor/v1sccor(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp),
& v2sccor(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp),
- & v0sccor(maxterm_sccor,-ntyp:ntyp),
+ & v0sccor(-ntyp:ntyp,-ntyp:ntyp),
& nterm_sccor(-ntyp:ntyp,-ntyp:ntyp),isccortyp(-ntyp:ntyp),
& nsccortyp,
& nlor_sccor(-ntyp:ntyp,-ntyp:ntyp),
& vlor1sccor(maxterm_sccor,20,20),
& vlor2sccor(maxterm_sccor,20,20),
& nterm_sccor(-ntyp:ntyp,-ntyp:ntyp),isccortyp(-ntyp:ntyp),
& nsccortyp,
& nlor_sccor(-ntyp:ntyp,-ntyp:ntyp),
& vlor1sccor(maxterm_sccor,20,20),
& vlor2sccor(maxterm_sccor,20,20),
- & vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,0:maxres2,10),
- & dcostau(3,3,3,maxres2),dsintau(3,3,3,maxres2),
- & dtauangle(3,3,3,maxres2),dcosomicron(3,3,3,maxres2),
- & domicron(3,3,3,maxres2)
+ & vlor3sccor(maxterm_sccor,20,20)
+C,gloc_sc(3,0:maxres2,10),
+C & dcostau(3,3,3,maxres2),dsintau(3,3,3,maxres2),
+C & dtauangle(3,3,3,maxres2),dcosomicron(3,3,3,maxres2),
+C & domicron(3,3,3,maxres2)
diff --git
a/source/unres/src_MD/checkder_p.F
b/source/unres/src_MD/checkder_p.F
index
4d0379e
..
ff70fa1
100644
(file)
--- a/
source/unres/src_MD/checkder_p.F
+++ b/
source/unres/src_MD/checkder_p.F
@@
-284,7
+284,7
@@
C Check the gradient of the energy in Cartesian coordinates.
c call intcartderiv
c call checkintcartgrad
call zerograd
c call intcartderiv
c call checkintcartgrad
call zerograd
- aincr=1.0D-5
+ aincr=1.0D-6
write(iout,*) 'Calling CHECK_ECARTINT.'
nf=0
icall=0
write(iout,*) 'Calling CHECK_ECARTINT.'
nf=0
icall=0
diff --git
a/source/unres/src_MD/energy_p_new_barrier.F
b/source/unres/src_MD/energy_p_new_barrier.F
index
0bcd6f3
..
3ef05a4
100644
(file)
--- a/
source/unres/src_MD/energy_p_new_barrier.F
+++ b/
source/unres/src_MD/energy_p_new_barrier.F
@@
-3023,6
+3023,9
@@
C
C Loop over i,i+2 and i,i+3 pairs of the peptide groups
C
do i=iturn3_start,iturn3_end
C Loop over i,i+2 and i,i+3 pairs of the peptide groups
C
do i=iturn3_start,iturn3_end
+ if (itype(i).eq.21 .or. itype(i+1).eq.21
+ & .or. itype(i+2).eq.21 .or. itype(i+3).eq.21.or.itype(i+4).eq.21)
+ & cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
@@
-3038,6
+3041,10
@@
C
num_cont_hb(i)=num_conti
enddo
do i=iturn4_start,iturn4_end
num_cont_hb(i)=num_conti
enddo
do i=iturn4_start,iturn4_end
+ if (itype(i).eq.21 .or. itype(i+1).eq.21
+ & .or. itype(i+2).eq.21 .or. itype(i+3).eq.21.or.itype(i+4).eq.21
+ & .or. itype(i+5).eq.21)
+ & cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
@@
-3056,6
+3063,8
@@
c
c Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3
c
do i=iatel_s,iatel_e
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.21 .or. itype(i+1).eq.21
+ &.or.itype(i+2)) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
@@
-3068,6
+3077,8
@@
c
c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
num_conti=num_cont_hb(i)
do j=ielstart(i),ielend(i)
c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
num_conti=num_cont_hb(i)
do j=ielstart(i),ielend(i)
+ if (itype(j).eq.21 .or. itype(j+1).eq.21
+ &.or.itype(j+2)) cycle
call eelecij(i,j,ees,evdw1,eel_loc)
enddo ! j
num_cont_hb(i)=num_conti
call eelecij(i,j,ees,evdw1,eel_loc)
enddo ! j
num_cont_hb(i)=num_conti
@@
-5959,17
+5970,19
@@
c lprn=.true.
c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
esccor=0.0D0
do i=itau_start,itau_end
c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
esccor=0.0D0
do i=itau_start,itau_end
+C do i=42,42
esccor_ii=0.0D0
if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle
isccori=isccortyp(itype(i-2))
isccori1=isccortyp(itype(i-1))
phii=phi(i)
esccor_ii=0.0D0
if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle
isccori=isccortyp(itype(i-2))
isccori1=isccortyp(itype(i-1))
phii=phi(i)
+
cccc Added 9 May 2012
cc Tauangle is torsional engle depending on the value of first digit
c(see comment below)
cc Omicron is flat angle depending on the value of first digit
c(see comment below)
cccc Added 9 May 2012
cc Tauangle is torsional engle depending on the value of first digit
c(see comment below)
cc Omicron is flat angle depending on the value of first digit
c(see comment below)
-
+C print *,i,tauangle(1,i)
do intertyp=1,3 !intertyp
cc Added 09 May 2012 (Adasko)
do intertyp=1,3 !intertyp
cc Added 09 May 2012 (Adasko)
@@
-5996,6
+6009,7
@@
c 3 = SC...Ca...Ca...SCi
esccor=esccor+v1ij*cosphi+v2ij*sinphi
gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
enddo
esccor=esccor+v1ij*cosphi+v2ij*sinphi
gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
enddo
+C print *,i,tauangle(1,i),gloci
gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
c write (iout,*) "WTF",intertyp,i,itype(i),v1ij*cosphi+v2ij*sinphi
c &gloc_sc(intertyp,i-3,icg)
gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
c write (iout,*) "WTF",intertyp,i,itype(i),v1ij*cosphi+v2ij*sinphi
c &gloc_sc(intertyp,i-3,icg)
diff --git
a/source/unres/src_MD/intcartderiv.F
b/source/unres/src_MD/intcartderiv.F
index
889bedd
..
fcc2e86
100644
(file)
--- a/
source/unres/src_MD/intcartderiv.F
+++ b/
source/unres/src_MD/intcartderiv.F
@@
-35,7
+35,7
@@
c We need dtheta(:,:,i-1) to compute dphi(:,:,i)
do i=3,nres
#endif
cost=dcos(theta(i))
do i=3,nres
#endif
cost=dcos(theta(i))
- sint=sqrt(1-cost*cost)
+ sint=dsqrt(1-cost*cost)
do j=1,3
dcostheta(j,1,i)=-(dc_norm(j,i-1)+cost*dc_norm(j,i-2))/
& vbld(i-1)
do j=1,3
dcostheta(j,1,i)=-(dc_norm(j,i-1)+cost*dc_norm(j,i-2))/
& vbld(i-1)
@@
-54,9
+54,9
@@
c We need dtheta(:,:,i-1) to compute dphi(:,:,i)
#endif
if ((itype(i-1).ne.10).and.(itype(i-1).ne.21)) then
cost1=dcos(omicron(1,i))
#endif
if ((itype(i-1).ne.10).and.(itype(i-1).ne.21)) then
cost1=dcos(omicron(1,i))
- sint1=sqrt(1-cost1*cost1)
+ sint1=dsqrt(1-cost1*cost1)
cost2=dcos(omicron(2,i))
cost2=dcos(omicron(2,i))
- sint2=sqrt(1-cost2*cost2)
+ sint2=dsqrt(1-cost2*cost2)
do j=1,3
CC Calculate derivative over first omicron (Cai-2,Cai-1,SCi-1)
dcosomicron(j,1,1,i)=-(dc_norm(j,i-1+nres)+
do j=1,3
CC Calculate derivative over first omicron (Cai-2,Cai-1,SCi-1)
dcosomicron(j,1,1,i)=-(dc_norm(j,i-1+nres)+
@@
-149,7
+149,7
@@
c Obtaining the gamma derivatives from cosine derivative
endif
enddo
endif
enddo
- do i=1,nres-1
+ do i=1,nres
do j=1,3
dc_norm2(j,i+nres)=-dc_norm(j,i+nres)
enddo
do j=1,3
dc_norm2(j,i+nres)=-dc_norm(j,i+nres)
enddo
@@
-213,15
+213,15
@@
c Obtaining the gamma derivatives from cosine derivative
dcostau(j,1,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3*
& dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1)-scalp*
& (dc_norm2(j,i-2+nres)))/vbld(i-2+nres)
dcostau(j,1,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3*
& dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1)-scalp*
& (dc_norm2(j,i-2+nres)))/vbld(i-2+nres)
- dtauangle(j,1,1,i)=-1/sing*dcostau(j,1,1,i)
+ dtauangle(j,1,1,i)=-1.0d0/sing*dcostau(j,1,1,i)
dcostau(j,1,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2*
& dcostheta(j,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4*
& dcostheta(j,1,i)
dcostau(j,1,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2*
& dcostheta(j,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4*
& dcostheta(j,1,i)
- dtauangle(j,1,2,i)=-1/sing*dcostau(j,1,2,i)
+ dtauangle(j,1,2,i)=-1.0d0/sing*dcostau(j,1,2,i)
dcostau(j,1,3,i)=fac2*dcostheta(j,2,i)+fac4*
& dcostheta(j,2,i)-fac0*(-dc_norm(j,i-2+nres)-scalp*
& dc_norm(j,i-1))/vbld(i)
dcostau(j,1,3,i)=fac2*dcostheta(j,2,i)+fac4*
& dcostheta(j,2,i)-fac0*(-dc_norm(j,i-2+nres)-scalp*
& dc_norm(j,i-1))/vbld(i)
- dtauangle(j,1,3,i)=-1/sing*dcostau(j,1,3,i)
+ dtauangle(j,1,3,i)=-1.0d0/sing*dcostau(j,1,3,i)
c write (iout,*) "else",i
enddo
endif
c write (iout,*) "else",i
enddo
endif
@@
-287,15
+287,15
@@
c Obtaining the gamma derivatives from cosine derivative
dcostau(j,2,1,i)=fac1*dcostheta(j,1,i-1)+fac3*
& dcostheta(j,1,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp*
& dc_norm(j,i-3))/vbld(i-2)
dcostau(j,2,1,i)=fac1*dcostheta(j,1,i-1)+fac3*
& dcostheta(j,1,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp*
& dc_norm(j,i-3))/vbld(i-2)
- dtauangle(j,2,1,i)=-1/sing*dcostau(j,2,1,i)
+ dtauangle(j,2,1,i)=-1.0d0/sing*dcostau(j,2,1,i)
dcostau(j,2,2,i)=fac1*dcostheta(j,2,i-1)+fac2*
& dcosomicron(j,1,1,i)+fac3*dcostheta(j,2,i-1)+fac4*
& dcosomicron(j,1,1,i)
dcostau(j,2,2,i)=fac1*dcostheta(j,2,i-1)+fac2*
& dcosomicron(j,1,1,i)+fac3*dcostheta(j,2,i-1)+fac4*
& dcosomicron(j,1,1,i)
- dtauangle(j,2,2,i)=-1/sing*dcostau(j,2,2,i)
+ dtauangle(j,2,2,i)=-1.0d0/sing*dcostau(j,2,2,i)
dcostau(j,2,3,i)=fac2*dcosomicron(j,1,2,i)+fac4*
& dcosomicron(j,1,2,i)-fac0*(dc_norm(j,i-3)-scalp*
& dc_norm(j,i-1+nres))/vbld(i-1+nres)
dcostau(j,2,3,i)=fac2*dcosomicron(j,1,2,i)+fac4*
& dcosomicron(j,1,2,i)-fac0*(dc_norm(j,i-3)-scalp*
& dc_norm(j,i-1+nres))/vbld(i-1+nres)
- dtauangle(j,2,3,i)=-1/sing*dcostau(j,2,3,i)
+ dtauangle(j,2,3,i)=-1.0d0/sing*dcostau(j,2,3,i)
c write(iout,*) i,j,"else", dtauangle(j,2,3,i)
enddo
endif
c write(iout,*) i,j,"else", dtauangle(j,2,3,i)
enddo
endif
@@
-360,15
+360,15
@@
c Obtaining the gamma derivatives from cosine derivative
dcostau(j,3,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3*
& dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp*
& dc_norm2(j,i-2+nres))/vbld(i-2+nres)
dcostau(j,3,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3*
& dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp*
& dc_norm2(j,i-2+nres))/vbld(i-2+nres)
- dtauangle(j,3,1,i)=-1/sing*dcostau(j,3,1,i)
+ dtauangle(j,3,1,i)=-1.0d0/sing*dcostau(j,3,1,i)
dcostau(j,3,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2*
& dcosomicron(j,1,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4*
& dcosomicron(j,1,1,i)
dcostau(j,3,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2*
& dcosomicron(j,1,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4*
& dcosomicron(j,1,1,i)
- dtauangle(j,3,2,i)=-1/sing*dcostau(j,3,2,i)
+ dtauangle(j,3,2,i)=-1.0d0/sing*dcostau(j,3,2,i)
dcostau(j,3,3,i)=fac2*dcosomicron(j,1,2,i)+fac4*
& dcosomicron(j,1,2,i)-fac0*(dc_norm2(j,i-2+nres)-scalp*
& dc_norm(j,i-1+nres))/vbld(i-1+nres)
dcostau(j,3,3,i)=fac2*dcosomicron(j,1,2,i)+fac4*
& dcosomicron(j,1,2,i)-fac0*(dc_norm2(j,i-2+nres)-scalp*
& dc_norm(j,i-1+nres))/vbld(i-1+nres)
- dtauangle(j,3,3,i)=-1/sing*dcostau(j,3,3,i)
+ dtauangle(j,3,3,i)=-1.0d0/sing*dcostau(j,3,3,i)
c write(iout,*) "else",i
enddo
endif
c write(iout,*) "else",i
enddo
endif
diff --git
a/source/unres/src_MD/unres.F
b/source/unres/src_MD/unres.F
index
b14c040
..
a63047f
100644
(file)
--- a/
source/unres/src_MD/unres.F
+++ b/
source/unres/src_MD/unres.F
@@
-736,6
+736,7
@@
c enddo
print *,'icheckgrad=',icheckgrad
goto (10,20,30) icheckgrad
10 call check_ecartint
print *,'icheckgrad=',icheckgrad
goto (10,20,30) icheckgrad
10 call check_ecartint
+ call check_ecartint
return
20 call check_cartgrad
return
return
20 call check_cartgrad
return