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chyba dzialajacy lipid
author
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Thu, 19 Mar 2015 09:43:55 +0000
(10:43 +0100)
committer
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Thu, 19 Mar 2015 09:43:55 +0000
(10:43 +0100)
source/unres/src_MD-M/COMMON.SCCOR
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source/unres/src_MD-M/MD_A-MTS.F
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source/unres/src_MD-M/energy_p_new_barrier.F
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source/unres/src_MD-M/initialize_p.F
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source/unres/src_MD-M/parmread.F
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diff --git
a/source/unres/src_MD-M/COMMON.SCCOR
b/source/unres/src_MD-M/COMMON.SCCOR
index
7952bd1
..
b3e6a6d
100644
(file)
--- a/
source/unres/src_MD-M/COMMON.SCCOR
+++ b/
source/unres/src_MD-M/COMMON.SCCOR
@@
-12,7
+12,7
@@
cc Parameters of the SCCOR term
& nlor_sccor(-ntyp:ntyp,-ntyp:ntyp),
& vlor1sccor(maxterm_sccor,20,20),
& vlor2sccor(maxterm_sccor,20,20),
& 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),
+ & vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,-1: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)
& 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)
diff --git
a/source/unres/src_MD-M/MD_A-MTS.F
b/source/unres/src_MD-M/MD_A-MTS.F
index
30f6ab1
..
2dc00c1
100644
(file)
--- a/
source/unres/src_MD-M/MD_A-MTS.F
+++ b/
source/unres/src_MD-M/MD_A-MTS.F
@@
-230,6
+230,7
@@
c Variable time step algorithm.
#endif
endif
if (mod(itime,ntwx).eq.0) then
#endif
endif
if (mod(itime,ntwx).eq.0) then
+ write(iout,*) 'time=',itime
C call check_ecartint
call returnbox
write (tytul,'("time",f8.2)') totT
C call check_ecartint
call returnbox
write (tytul,'("time",f8.2)') totT
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
931f56f
..
0044ec5
100644
(file)
--- a/
source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/
source/unres/src_MD-M/energy_p_new_barrier.F
@@
-1623,7
+1623,7
@@
C what fraction I am in
C lipbufthick is thickenes of lipid buffore
sslipj=sscalelip(fracinbuf)
ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
C lipbufthick is thickenes of lipid buffore
sslipj=sscalelip(fracinbuf)
ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
- elseif (zi.gt.bufliptop) then
+ elseif (zj.gt.bufliptop) then
fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
sslipj=sscalelip(fracinbuf)
ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
sslipj=sscalelip(fracinbuf)
ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
@@
-1825,12
+1825,12
@@
C the energy transfer exist
if (zi.lt.buflipbot) then
C what fraction I am in
fracinbuf=1.0d0-
if (zi.lt.buflipbot) then
C what fraction I am in
fracinbuf=1.0d0-
- & ((positi-bordlipbot)/lipbufthick)
+ & ((zi-bordlipbot)/lipbufthick)
C lipbufthick is thickenes of lipid buffore
sslipi=sscalelip(fracinbuf)
ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
elseif (zi.gt.bufliptop) then
C lipbufthick is thickenes of lipid buffore
sslipi=sscalelip(fracinbuf)
ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
elseif (zi.gt.bufliptop) then
- fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
sslipi=sscalelip(fracinbuf)
ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
else
sslipi=sscalelip(fracinbuf)
ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
else
@@
-1893,12
+1893,12
@@
C the energy transfer exist
if (zj.lt.buflipbot) then
C what fraction I am in
fracinbuf=1.0d0-
if (zj.lt.buflipbot) then
C what fraction I am in
fracinbuf=1.0d0-
- & ((positi-bordlipbot)/lipbufthick)
+ & ((zj-bordlipbot)/lipbufthick)
C lipbufthick is thickenes of lipid buffore
sslipj=sscalelip(fracinbuf)
ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
C lipbufthick is thickenes of lipid buffore
sslipj=sscalelip(fracinbuf)
ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
- elseif (zi.gt.bufliptop) then
- fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
sslipj=sscalelip(fracinbuf)
ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
else
sslipj=sscalelip(fracinbuf)
ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
else
@@
-5143,7
+5143,6
@@
cgrad enddo
ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
enddo
endif
ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
enddo
endif
- endif
enddo
ehpb=0.5D0*ehpb
return
enddo
ehpb=0.5D0*ehpb
return
diff --git
a/source/unres/src_MD-M/initialize_p.F
b/source/unres/src_MD-M/initialize_p.F
index
17e59a8
..
2a6180a
100644
(file)
--- a/
source/unres/src_MD-M/initialize_p.F
+++ b/
source/unres/src_MD-M/initialize_p.F
@@
-256,20
+256,30
@@
C Initialize the bridge arrays
jhpb(i)=0
enddo
C Initialize correlation arrays
jhpb(i)=0
enddo
C Initialize correlation arrays
- do i=-maxtor,maxtor
+ do i=1,maxres
do k=1,2
b1(k,i)=0.0
b2(k,i)=0.0
b1tilde(k,i)=0.0
c b2tilde(k,i)=0.0
do j=1,2
do k=1,2
b1(k,i)=0.0
b2(k,i)=0.0
b1tilde(k,i)=0.0
c b2tilde(k,i)=0.0
do j=1,2
+C CC(j,k,i)=0.0
+C Ctilde(j,k,i)=0.0
+C DD(j,k,i)=0.0
+C Dtilde(j,k,i)=0.0
+ EE(j,k,i)=0.0
+ enddo
+ enddo
+ enddo
+ do i=-maxtor,maxtor
+ do k=1,2
+ do j=1,2
CC(j,k,i)=0.0
Ctilde(j,k,i)=0.0
DD(j,k,i)=0.0
Dtilde(j,k,i)=0.0
CC(j,k,i)=0.0
Ctilde(j,k,i)=0.0
DD(j,k,i)=0.0
Dtilde(j,k,i)=0.0
- EE(j,k,i)=0.0
enddo
enddo
- enddo
+ enddo
enddo
C
C Initialize timing.
enddo
C
C Initialize timing.
diff --git
a/source/unres/src_MD-M/parmread.F
b/source/unres/src_MD-M/parmread.F
index
9ba2044
..
5d45e14
100644
(file)
--- a/
source/unres/src_MD-M/parmread.F
+++ b/
source/unres/src_MD-M/parmread.F
@@
-1006,6
+1006,7
@@
c Dtilde(2,2,i)=0.0d0
EEold(2,1,-i)=-b(12,i)+b(13,i)
EEold(1,2,-i)=-b(12,i)-b(13,i)
write(iout,*) "TU DOCHODZE"
EEold(2,1,-i)=-b(12,i)+b(13,i)
EEold(1,2,-i)=-b(12,i)-b(13,i)
write(iout,*) "TU DOCHODZE"
+ print *,"JESTEM"
c ee(1,1,i)=1.0d0
c ee(2,2,i)=1.0d0
c ee(2,1,i)=0.0d0
c ee(1,1,i)=1.0d0
c ee(2,2,i)=1.0d0
c ee(2,1,i)=0.0d0
@@
-1118,7
+1119,7
@@
C now we start reading lipid
read (isidep,*,end=1161,err=1161)(epslip(i,j),j=i,ntyp)
print *,"WARNING!!"
do j=1,ntyp
read (isidep,*,end=1161,err=1161)(epslip(i,j),j=i,ntyp)
print *,"WARNING!!"
do j=1,ntyp
- epslip(i,j)=epslip(i,j)+0.5d0
+ epslip(i,j)=epslip(i,j)+0.05d0
enddo
enddo
C For the GB potential convert sigma'**2 into chi'
enddo
enddo
C For the GB potential convert sigma'**2 into chi'