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Merge branch 'adasko' of mmka.chem.univ.gda.pl:unres into adasko
[unres.git]
/
source
/
unres
/
src_MD-M
/
MD_A-MTS.F
diff --git
a/source/unres/src_MD-M/MD_A-MTS.F
b/source/unres/src_MD-M/MD_A-MTS.F
index
6c6fb14
..
e0c1cfb
100644
(file)
--- a/
source/unres/src_MD-M/MD_A-MTS.F
+++ b/
source/unres/src_MD-M/MD_A-MTS.F
@@
-209,7
+209,7
@@
c Variable time step algorithm.
enddo
enddo
do i=nnt,nct
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
ind=ind+1
v_work(ind)=d_t(j,i+nres)
do j=1,3
ind=ind+1
v_work(ind)=d_t(j,i+nres)
@@
-232,6
+232,7
@@
c Variable time step algorithm.
if (mod(itime,ntwx).eq.0) then
write (tytul,'("time",f8.2)') totT
if(mdpdb) then
if (mod(itime,ntwx).eq.0) then
write (tytul,'("time",f8.2)') totT
if(mdpdb) then
+ call check_ecartint
call hairpin(.true.,nharp,iharp)
call secondary2(.true.)
call pdbout(potE,tytul,ipdb)
call hairpin(.true.,nharp,iharp)
call secondary2(.true.)
call pdbout(potE,tytul,ipdb)
@@
-955,7
+956,7
@@
c forces).
enddo
enddo
do i=nnt,nct
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t(j,inres)+0.5d0*d_a(j,inres)*d_time
inres=i+nres
do j=1,3
d_t(j,inres)=d_t(j,inres)+0.5d0*d_a(j,inres)*d_time
@@
-1005,7
+1006,7
@@
c Applying velocity Verlet algorithm - step 1 to coordinates
enddo
enddo
do i=nnt,nct
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
adt=d_a_old(j,inres)*d_time
inres=i+nres
do j=1,3
adt=d_a_old(j,inres)*d_time
@@
-1049,7
+1050,7
@@
c Step 2 of the velocity Verlet algorithm: update velocities
enddo
enddo
do i=nnt,nct
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_new(j,inres)+0.5d0*d_a(j,inres)*d_time
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_new(j,inres)+0.5d0*d_a(j,inres)*d_time
@@
-1148,7
+1149,7
@@
c
ind=ind+3
enddo
do i=nnt,nct
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
adt=(d_a_old(j,inres)+d_af_work(ind+j))*d_time
inres=i+nres
do j=1,3
adt=(d_a_old(j,inres)+d_af_work(ind+j))*d_time
@@
-1213,7
+1214,7
@@
c
ind=ind+3
enddo
do i=nnt,nct
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_new(j,inres)+(0.5d0*(d_a(j,inres)
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_new(j,inres)+(0.5d0*(d_a(j,inres)
@@
-1260,6
+1261,7
@@
c accel(j)=aux(j)+0.5d0*(d_a(j,i)-d_a_old(j,i))
c if (dabs(accel(j)).gt.amax) amax=dabs(accel(j))
if (dabs(accel(j)).gt.dabs(accel_old(j))) then
dacc=dabs(accel(j)-accel_old(j))
c if (dabs(accel(j)).gt.amax) amax=dabs(accel(j))
if (dabs(accel(j)).gt.dabs(accel_old(j))) then
dacc=dabs(accel(j)-accel_old(j))
+c write (iout,*) i,dacc
if (dacc.gt.amax) amax=dacc
endif
enddo
if (dacc.gt.amax) amax=dacc
endif
enddo
@@
-1278,7
+1280,7
@@
c accel(j)=aux(j)
enddo
endif
do i=nnt,nct
enddo
endif
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
c accel(j)=accel(j)+d_a(j,i+nres)-d_a_old(j,i+nres)
accel_old(j)=accel_old(j)+d_a_old(j,i+nres)
do j=1,3
c accel(j)=accel(j)+d_a(j,i+nres)-d_a_old(j,i+nres)
accel_old(j)=accel_old(j)+d_a_old(j,i+nres)
@@
-1289,6
+1291,7
@@
c accel(j)=accel(j)+d_a(j,i+nres)-d_a_old(j,i+nres)
c if (dabs(accel(j)).gt.amax) amax=dabs(accel(j))
if (dabs(accel(j)).gt.dabs(accel_old(j))) then
dacc=dabs(accel(j)-accel_old(j))
c if (dabs(accel(j)).gt.amax) amax=dabs(accel(j))
if (dabs(accel(j)).gt.dabs(accel_old(j))) then
dacc=dabs(accel(j)-accel_old(j))
+c write (iout,*) "side-chain",i,dacc
if (dacc.gt.amax) amax=dacc
endif
enddo
if (dacc.gt.amax) amax=dacc
endif
enddo
@@
-1331,7
+1334,7
@@
c write (iout,*) "back",i,j,epdriftij
enddo
endif
c Side chains
enddo
endif
c Side chains
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
epdriftij=
& dabs((d_a(j,i+nres)-d_a_old(j,i+nres))*gxcart(j,i))
do j=1,3
epdriftij=
& dabs((d_a(j,i+nres)-d_a_old(j,i+nres))*gxcart(j,i))
@@
-1378,7
+1381,7
@@
c write(iout,*) "fact", fact
enddo
enddo
do i=nnt,nct
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
d_t(j,inres)=fact*d_t(j,inres)
inres=i+nres
do j=1,3
d_t(j,inres)=fact*d_t(j,inres)
@@
-1433,7
+1436,8
@@
c if the friction coefficients do not depend on surface area
stdforcp(i)=stdfp*dsqrt(gamp)
enddo
do i=nnt,nct
stdforcp(i)=stdfp*dsqrt(gamp)
enddo
do i=nnt,nct
- stdforcsc(i)=stdfsc(itype(i))*dsqrt(gamsc(itype(i)))
+ stdforcsc(i)=stdfsc(iabs(itype(i)))
+ & *dsqrt(gamsc(iabs(itype(i))))
enddo
endif
c Open the pdb file for snapshotshots
enddo
endif
c Open the pdb file for snapshotshots
@@
-1605,7
+1609,7
@@
c Removing the velocity of the center of mass
call chainbuild_cart
call kinetic(EK)
if (tbf) then
call chainbuild_cart
call kinetic(EK)
if (tbf) then
- call verlet_bath(EK)
+ call verlet_bath
endif
kinetic_T=2.0d0/(dimen3*Rb)*EK
if(me.eq.king.or..not.out1file)then
endif
kinetic_T=2.0d0/(dimen3*Rb)*EK
if(me.eq.king.or..not.out1file)then
@@
-1824,7
+1828,7
@@
c Transfer to the d_t vector
enddo
enddo
do i=nnt,nct
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
ind=ind+1
d_t(j,i+nres)=d_t_work(ind)
do j=1,3
ind=ind+1
d_t(j,i+nres)=d_t_work(ind)
@@
-2053,7
+2057,7
@@
c enddo
ind=ind+3
enddo
do i=nnt,nct
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
dc_work(ind+j)=dc_old(j,i+nres)
d_t_work(ind+j)=d_t_old(j,i+nres)
do j=1,3
dc_work(ind+j)=dc_old(j,i+nres)
d_t_work(ind+j)=d_t_old(j,i+nres)
@@
-2162,7
+2166,7
@@
c
ind=ind+3
enddo
do i=nnt,nct
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_work(ind+j)
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_work(ind+j)
@@
-2319,7
+2323,7
@@
c enddo
ind=ind+3
enddo
do i=nnt,nct
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
dc_work(ind+j)=dc_old(j,i+nres)
d_t_work(ind+j)=d_t_old(j,i+nres)
do j=1,3
dc_work(ind+j)=dc_old(j,i+nres)
d_t_work(ind+j)=d_t_old(j,i+nres)
@@
-2368,7
+2372,7
@@
c enddo
ind=ind+3
enddo
do i=nnt,nct
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
dc(j,inres)=dc_work(ind+j)
inres=i+nres
do j=1,3
dc(j,inres)=dc_work(ind+j)
@@
-2429,7
+2433,7
@@
c ddt2=ddt2+vrand_mat2(i,j)*stochforcvecV(j)
ind=ind+3
enddo
do i=nnt,nct
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_work(ind+j)
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_work(ind+j)