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dzialajacy wham+poprawka w funckji energi+ poprawka w czytaniu
author
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Mon, 19 Jan 2015 13:32:01 +0000
(14:32 +0100)
committer
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Mon, 19 Jan 2015 13:32:01 +0000
(14:32 +0100)
source/cluster/wham/src-M/energy_p_new.F
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source/unres/src_MD-M/energy_p_new_barrier.F
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source/unres/src_MD-M/refsys.f
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source/wham/src-M/enecalc1.F
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source/wham/src-M/energy_p_new.F
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source/wham/src-M/readpdb.f
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diff --git
a/source/cluster/wham/src-M/energy_p_new.F
b/source/cluster/wham/src-M/energy_p_new.F
index
d6ea982
..
c7c2c2f
100644
(file)
--- a/
source/cluster/wham/src-M/energy_p_new.F
+++ b/
source/cluster/wham/src-M/energy_p_new.F
@@
-3045,7
+3045,7
@@
c write (iout,*) i,vbld(i),vbldp0,diff,AKP*diff*diff
endif
enddo
endif
enddo
- estr=0.5d0*AKP*estr
+ estr=0.5d0*AKP*estr+estr1
c
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
c
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
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
eae81d8
..
539102b
100644
(file)
--- a/
source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/
source/unres/src_MD-M/energy_p_new_barrier.F
@@
-5559,7
+5559,8
@@
c lprn=.true.
etors=0.0D0
do i=iphi_start,iphi_end
if (itype(i-2).eq.21 .or. itype(i-1).eq.21
etors=0.0D0
do i=iphi_start,iphi_end
if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
+ & .or. itype(i).eq.21
+ & .or. itype(i-3).eq.ntyp1) cycle
etors_ii=0.0D0
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
etors_ii=0.0D0
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
@@
-5655,7
+5656,8
@@
c lprn=.true.
C write(iout,*) "a tu??"
do i=iphid_start,iphid_end
if (itype(i-2).eq.21 .or. itype(i-1).eq.21
C write(iout,*) "a tu??"
do i=iphid_start,iphid_end
if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ & .or. itype(i).eq.21 .or. itype(i+1).eq.21
+ & .or. itype(i-3).eq.ntyp1) cycle
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
itori2=itortyp(itype(i))
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
itori2=itortyp(itype(i))
diff --git
a/source/unres/src_MD-M/refsys.f
b/source/unres/src_MD-M/refsys.f
index
86b0524
..
8c58a82
100644
(file)
--- a/
source/unres/src_MD-M/refsys.f
+++ b/
source/unres/src_MD-M/refsys.f
@@
-1,4
+1,4
@@
- subroutine refsys(fail)
+ subroutine refsys(i2,i3,i4,e1,e2,e3,fail)
c This subroutine calculates unit vectors of a local reference system
c defined by atoms (i2), (i3), and (i4). The x axis is the axis from
c atom (i3) to atom (i2), and the xy plane is the plane defined by atoms
c This subroutine calculates unit vectors of a local reference system
c defined by atoms (i2), (i3), and (i4). The x axis is the axis from
c atom (i3) to atom (i2), and the xy plane is the plane defined by atoms
diff --git
a/source/wham/src-M/enecalc1.F
b/source/wham/src-M/enecalc1.F
index
5ce2fff
..
880664c
100644
(file)
--- a/
source/wham/src-M/enecalc1.F
+++ b/
source/wham/src-M/enecalc1.F
@@
-201,6
+201,10
@@
c call pdbout(ii+1,beta_h(ib,ipar),efree,energia(0),0.0d0,rmsdev)
& " the value read in: ",energia(0),eini," point",
& iii+1,indstart(me1)+iii," T",
& 1.0d0/(1.987D-3*beta_h(ib,ipar))
& " the value read in: ",energia(0),eini," point",
& iii+1,indstart(me1)+iii," T",
& 1.0d0/(1.987D-3*beta_h(ib,ipar))
+ call pdbout(indstart(me1)+iii,
+ & 1.0d0/(1.987D-3*beta_h(ib,ipar)),
+ &energia(0),eini,0.0d0,0.0d0)
+ call enerprint(energia(0),fT)
errmsg_count=errmsg_count+1
if (errmsg_count.gt.maxerrmsg_count)
& write (iout,*) "Too many warning messages"
errmsg_count=errmsg_count+1
if (errmsg_count.gt.maxerrmsg_count)
& write (iout,*) "Too many warning messages"
diff --git
a/source/wham/src-M/energy_p_new.F
b/source/wham/src-M/energy_p_new.F
index
b5e9340
..
af921d0
100644
(file)
--- a/
source/wham/src-M/energy_p_new.F
+++ b/
source/wham/src-M/energy_p_new.F
@@
-3095,7
+3095,7
@@
c write (iout,*) i,vbld(i),vbldp0,diff,AKP*diff*diff
endif
enddo
endif
enddo
- estr=0.5d0*AKP*estr
+ estr=0.5d0*AKP*estr+estr1
c
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
c
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
@@
-4360,7
+4360,8
@@
c lprn=.true.
etors=0.0D0
do i=iphi_start,iphi_end
if (itype(i-2).eq.21 .or. itype(i-1).eq.21
etors=0.0D0
do i=iphi_start,iphi_end
if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
+ & .or. itype(i).eq.21
+ & .or. itype(i-3).eq.ntyp1) cycle
if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
@@
-4454,7
+4455,8
@@
c lprn=.true.
etors_d=0.0D0
do i=iphi_start,iphi_end-1
if (itype(i-2).eq.21 .or. itype(i-1).eq.21
etors_d=0.0D0
do i=iphi_start,iphi_end-1
if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ & .or. itype(i).eq.21 .or. itype(i+1).eq.21
+ & .or. itype(i-3).eq.ntyp1) cycle
if (itel(i-2).eq.0 .or. itel(i-1).eq.0 .or. itel(i).eq.0)
& goto 1215
itori=itortyp(itype(i-2))
if (itel(i-2).eq.0 .or. itel(i-1).eq.0 .or. itel(i).eq.0)
& goto 1215
itori=itortyp(itype(i-2))
diff --git
a/source/wham/src-M/readpdb.f
b/source/wham/src-M/readpdb.f
index
93c9cbe
..
fa2d05d
100644
(file)
--- a/
source/wham/src-M/readpdb.f
+++ b/
source/wham/src-M/readpdb.f
@@
-173,17
+173,19
@@
c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
do j=1,3
cref(j,i,cou)=c(j,i)
cref(j,i+nres,cou)=c(j,i+nres)
do j=1,3
cref(j,i,cou)=c(j,i)
cref(j,i+nres,cou)=c(j,i+nres)
- if (i.le.nres) then
+ if ((i.le.nres).and.(symetr.gt.1)) then
chain_rep(j,lll,kkk)=c(j,i)
chain_rep(j,lll+nres,kkk)=c(j,i+nres)
endif
enddo
enddo
chain_rep(j,lll,kkk)=c(j,i)
chain_rep(j,lll+nres,kkk)=c(j,i+nres)
endif
enddo
enddo
+ if (symetr.gt.1) then
do j=1,3
chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
chain_rep(j,chain_length+nres,symetr)
&=chain_rep(j,chain_length+nres,1)
enddo
do j=1,3
chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
chain_rep(j,chain_length+nres,symetr)
&=chain_rep(j,chain_length+nres,1)
enddo
+ endif
c diagnostic
c diagnostic
c diagnostic
c diagnostic