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poprawki w potencjalach
author
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Wed, 18 Mar 2015 12:45:34 +0000
(13:45 +0100)
committer
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Wed, 18 Mar 2015 12:45:34 +0000
(13:45 +0100)
source/unres/src_MD-M/MD_A-MTS.F
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source/unres/src_MD-M/chainbuild.F
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source/unres/src_MD-M/checkder_p.F
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source/unres/src_MD-M/energy_p_new_barrier.F
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source/unres/src_MD-M/gradient_p.F
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diff --git
a/source/unres/src_MD-M/MD_A-MTS.F
b/source/unres/src_MD-M/MD_A-MTS.F
index
6154487
..
30f6ab1
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
+C call check_ecartint
call returnbox
write (tytul,'("time",f8.2)') totT
if(mdpdb) then
call returnbox
write (tytul,'("time",f8.2)') totT
if(mdpdb) then
@@
-997,6
+998,8
@@
c Applying velocity Verlet algorithm - step 1 to coordinates
d_t(j,0)=d_t_old(j,0)+adt
enddo
do i=nnt,nct-1
d_t(j,0)=d_t_old(j,0)+adt
enddo
do i=nnt,nct-1
+C SPYTAC ADAMA
+C do i=0,nres
do j=1,3
adt=d_a_old(j,i)*d_time
adt2=0.5d0*adt
do j=1,3
adt=d_a_old(j,i)*d_time
adt2=0.5d0*adt
@@
-1006,6
+1009,7
@@
c Applying velocity Verlet algorithm - step 1 to coordinates
enddo
enddo
do i=nnt,nct
enddo
enddo
do i=nnt,nct
+C do i=0,nres
if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
diff --git
a/source/unres/src_MD-M/chainbuild.F
b/source/unres/src_MD-M/chainbuild.F
index
766e14a
..
c528ea5
100644
(file)
--- a/
source/unres/src_MD-M/chainbuild.F
+++ b/
source/unres/src_MD-M/chainbuild.F
@@
-19,6
+19,10
@@
C Set lprn=.true. for debugging
perbox=.false.
fail=.false.
print *, 'enter chainbuild'
perbox=.false.
fail=.false.
print *, 'enter chainbuild'
+ call chainbuild_cart
+ return
+ end
+#ifdef DEBUG
if (perbox) then
cost=dcos(theta(3))
sint=dsin(theta(3))
if (perbox) then
cost=dcos(theta(3))
sint=dsin(theta(3))
@@
-175,6
+179,7
@@
C
endif
return
end
endif
return
end
+#endif
c-------------------------------------------------------------------------
subroutine orig_frame
C
c-------------------------------------------------------------------------
subroutine orig_frame
C
diff --git
a/source/unres/src_MD-M/checkder_p.F
b/source/unres/src_MD-M/checkder_p.F
index
32d2366
..
99f00bc
100644
(file)
--- a/
source/unres/src_MD-M/checkder_p.F
+++ b/
source/unres/src_MD-M/checkder_p.F
@@
-395,6
+395,7
@@
c write (iout,*) "etot11",etot11," etot12",etot12
c write(iout,'(2i5,2(a,f15.10))')i,j," etot",etot," etot1",etot1
dc(j,i)=ddc(j)-aincr
call chainbuild_cart
c write(iout,'(2i5,2(a,f15.10))')i,j," etot",etot," etot1",etot1
dc(j,i)=ddc(j)-aincr
call chainbuild_cart
+C print *,c(j,i)
c call int_from_cart1(.false.)
if (.not.split_ene) then
call etotal(energia1(0))
c call int_from_cart1(.false.)
if (.not.split_ene) then
call etotal(energia1(0))
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
cbaadfb
..
e6f630d
100644
(file)
--- a/
source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/
source/unres/src_MD-M/energy_p_new_barrier.F
@@
-10141,7
+10141,8
@@
C lipbufthick is thickenes of lipid buffore
gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
-C print *,"doing sccale for lower part"
+C print *,"doing sccale for lower part"
+C print *,i,sslip,fracinbuf,ssgradlip
elseif (positi.gt.bufliptop) then
fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
sslip=sscalelip(fracinbuf)
elseif (positi.gt.bufliptop) then
fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
sslip=sscalelip(fracinbuf)
@@
-10151,6
+10152,7
@@
C print *,"doing sccale for lower part"
gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
C print *, "doing sscalefor top part"
gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
C print *, "doing sscalefor top part"
+C print *,i,sslip,fracinbuf,ssgradlip
else
eliptran=eliptran+pepliptran
C print *,"I am in true lipid"
else
eliptran=eliptran+pepliptran
C print *,"I am in true lipid"
@@
-10163,7
+10165,7
@@
C print *, "nic nie bylo w lipidzie?"
C now multiply all by the peptide group transfer factor
C eliptran=eliptran*pepliptran
C now the same for side chains
C now multiply all by the peptide group transfer factor
C eliptran=eliptran*pepliptran
C now the same for side chains
-C do i=1,1
+CV do i=1,1
do i=ilip_start,ilip_end
if (itype(i).eq.ntyp1) cycle
positi=(mod(c(3,i+nres),boxzsize))
do i=ilip_start,ilip_end
if (itype(i).eq.ntyp1) cycle
positi=(mod(c(3,i+nres),boxzsize))
@@
-10183,9
+10185,9
@@
C lipbufthick is thickenes of lipid buffore
ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
eliptran=eliptran+sslip*liptranene(itype(i))
gliptranx(3,i)=gliptranx(3,i)
ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
eliptran=eliptran+sslip*liptranene(itype(i))
gliptranx(3,i)=gliptranx(3,i)
- &+ssgradlip*liptranene(itype(i))/2.0d0
+ &+ssgradlip*liptranene(itype(i))
gliptranc(3,i-1)= gliptranc(3,i-1)
gliptranc(3,i-1)= gliptranc(3,i-1)
- &+ssgradlip*liptranene(itype(i))/2.0d0
+ &+ssgradlip*liptranene(itype(i))
C print *,"doing sccale for lower part"
elseif (positi.gt.bufliptop) then
fracinbuf=1.0d0-
C print *,"doing sccale for lower part"
elseif (positi.gt.bufliptop) then
fracinbuf=1.0d0-
@@
-10194,9
+10196,9
@@
C print *,"doing sccale for lower part"
ssgradlip=sscagradlip(fracinbuf)/lipbufthick
eliptran=eliptran+sslip*liptranene(itype(i))
gliptranx(3,i)=gliptranx(3,i)
ssgradlip=sscagradlip(fracinbuf)/lipbufthick
eliptran=eliptran+sslip*liptranene(itype(i))
gliptranx(3,i)=gliptranx(3,i)
- &+ssgradlip*liptranene(itype(i))/2.0d0
+ &+ssgradlip*liptranene(itype(i))
gliptranc(3,i-1)= gliptranc(3,i-1)
gliptranc(3,i-1)= gliptranc(3,i-1)
- &+ssgradlip*liptranene(itype(i))/2.0d0
+ &+ssgradlip*liptranene(itype(i))
C print *, "doing sscalefor top part",sslip,fracinbuf
else
eliptran=eliptran+liptranene(itype(i))
C print *, "doing sscalefor top part",sslip,fracinbuf
else
eliptran=eliptran+liptranene(itype(i))
diff --git
a/source/unres/src_MD-M/gradient_p.F
b/source/unres/src_MD-M/gradient_p.F
index
9b1856f
..
3d90077
100644
(file)
--- a/
source/unres/src_MD-M/gradient_p.F
+++ b/
source/unres/src_MD-M/gradient_p.F
@@
-381,6
+381,8
@@
C
gradx(j,i,icg)=0.0d0
gscloc(j,i)=0.0d0
gsclocx(j,i)=0.0d0
gradx(j,i,icg)=0.0d0
gscloc(j,i)=0.0d0
gsclocx(j,i)=0.0d0
+ gliptranc(j,i)=0.0d0
+ gliptranx(j,i)=0.0d0
do intertyp=1,3
gloc_sc(intertyp,i,icg)=0.0d0
enddo
do intertyp=1,3
gloc_sc(intertyp,i,icg)=0.0d0
enddo