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debug w poszukiwaniu bledu w ostatniej reszcie
author
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Fri, 19 Dec 2014 12:29:56 +0000
(13:29 +0100)
committer
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Fri, 19 Dec 2014 12:29:56 +0000
(13:29 +0100)
source/unres/src_MD-M/COMMON.TORSION
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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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source/unres/src_MD-M/int_to_cart.f
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source/unres/src_MD-M/parmread.F
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source/unres/src_MD-M/stochfric.F
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diff --git
a/source/unres/src_MD-M/COMMON.TORSION
b/source/unres/src_MD-M/COMMON.TORSION
index
2a887a6
..
e0f9c5d
100644
(file)
--- a/
source/unres/src_MD-M/COMMON.TORSION
+++ b/
source/unres/src_MD-M/COMMON.TORSION
@@
-10,7
+10,7
@@
C Torsional constants of the rotation about virtual-bond dihedral angles
& nterm(maxtor,maxtor),
& nlor(maxtor,maxtor),
& nterm_old,
& nterm(maxtor,maxtor),
& nlor(maxtor,maxtor),
& nterm_old,
- & itortyp(ntyp),
+ & itortyp(ntyp1),
& ntortyp
C 6/23/01 - constants for double torsionals
double precision v1c,v1s,v2c,v2s
& ntortyp
C 6/23/01 - constants for double torsionals
double precision v1c,v1s,v2c,v2s
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
b9d17fe
..
0c2f5ed
100644
(file)
--- a/
source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/
source/unres/src_MD-M/energy_p_new_barrier.F
@@
-85,7
+85,7
@@
C FG slaves receive the WEIGHTS array
time_Bcastw=time_Bcastw+MPI_Wtime()-time00
c call chainbuild_cart
endif
time_Bcastw=time_Bcastw+MPI_Wtime()-time00
c call chainbuild_cart
endif
-c print *,'Processor',myrank,' calling etotal ipot=',ipot
+C print *,'Processor',myrank,' calling etotal ipot=',ipot
c print *,'Processor',myrank,' nnt=',nnt,' nct=',nct
#else
c if (modecalc.eq.12.or.modecalc.eq.14) then
c print *,'Processor',myrank,' nnt=',nnt,' nct=',nct
#else
c if (modecalc.eq.12.or.modecalc.eq.14) then
@@
-98,6
+98,7
@@
c endif
C
C Compute the side-chain and electrostatic interaction energy
C
C
C Compute the side-chain and electrostatic interaction energy
C
+C write(iout,*) "zaczynam liczyc energie"
goto (101,102,103,104,105,106) ipot
C Lennard-Jones potential.
101 call elj(evdw)
goto (101,102,103,104,105,106) ipot
C Lennard-Jones potential.
101 call elj(evdw)
@@
-117,10
+118,13
@@
C Gay-Berne-Vorobjev potential (shifted LJ, angular dependence).
goto 107
C Soft-sphere potential
106 call e_softsphere(evdw)
goto 107
C Soft-sphere potential
106 call e_softsphere(evdw)
+C write(iout,*) "skonczylem ipoty"
+
C
C Calculate electrostatic (H-bonding) energy of the main chain.
C
107 continue
C
C Calculate electrostatic (H-bonding) energy of the main chain.
C
107 continue
+C write(iout,*) "skonczylem ipoty"
cmc
cmc Sep-06: egb takes care of dynamic ss bonds too
cmc
cmc
cmc Sep-06: egb takes care of dynamic ss bonds too
cmc
@@
-442,7
+446,6
@@
cMS$ATTRIBUTES C :: proc_proc
#endif
double precision gradbufc(3,maxres),gradbufx(3,maxres),
& glocbuf(4*maxres),gradbufc_sum(3,maxres),gloc_scbuf(3,maxres)
#endif
double precision gradbufc(3,maxres),gradbufx(3,maxres),
& glocbuf(4*maxres),gradbufc_sum(3,maxres),gloc_scbuf(3,maxres)
-#endif
include 'COMMON.SETUP'
include 'COMMON.IOUNITS'
include 'COMMON.FFIELD'
include 'COMMON.SETUP'
include 'COMMON.IOUNITS'
include 'COMMON.FFIELD'
@@
-2338,6
+2341,7
@@
C
endif
c if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then
if (i.gt. nnt+2 .and. i.lt.nct+2) then
endif
c if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then
if (i.gt. nnt+2 .and. i.lt.nct+2) then
+c write(iout,*) (itype(i-2))
iti = itortyp(itype(i-2))
else
iti=ntortyp+1
iti = itortyp(itype(i-2))
else
iti=ntortyp+1
@@
-2718,7
+2722,7
@@
C
dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3),
& erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3)
double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4),
dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3),
& erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3)
double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4),
- & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4)
+ & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4),eel_loc_ij
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
& dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
& num_conti,j1,j2
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
& dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
& num_conti,j1,j2
@@
-2761,6
+2765,7
@@
c call vec_and_deriv
time01=MPI_Wtime()
#endif
call set_matrices
time01=MPI_Wtime()
#endif
call set_matrices
+c write (iout,*) "after set matrices"
#ifdef TIMING
time_mat=time_mat+MPI_Wtime()-time01
#endif
#ifdef TIMING
time_mat=time_mat+MPI_Wtime()-time01
#endif
@@
-2797,6
+2802,7
@@
c 9/27/08 AL Split the interaction loop to ensure load balancing of turn terms
C
C Loop over i,i+2 and i,i+3 pairs of the peptide groups
C
C
C Loop over i,i+2 and i,i+3 pairs of the peptide groups
C
+c write(iout,*) "przed turnem3 loop"
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) cycle
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) cycle
@@
-2889,7
+2895,7
@@
C-------------------------------------------------------------------------------
dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3),
& erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3)
double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4),
dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3),
& erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3)
double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4),
- & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4)
+ & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4),a22,a23,a32,a33
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
& dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
& num_conti,j1,j2
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
& dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
& num_conti,j1,j2
@@
-3659,7
+3665,7
@@
c write (iout,*) "eturn4 i",i," j",j," j1",j1," j2",j2
iti1=itortyp(itype(i+1))
iti2=itortyp(itype(i+2))
iti3=itortyp(itype(i+3))
iti1=itortyp(itype(i+1))
iti2=itortyp(itype(i+2))
iti3=itortyp(itype(i+3))
-c write(iout,*) "iti1",iti1," iti2",iti2," iti3",iti3
+ write(iout,*) "iti1",iti1," iti2",iti2," iti3",iti3
call transpose2(EUg(1,1,i+1),e1t(1,1))
call transpose2(Eug(1,1,i+2),e2t(1,1))
call transpose2(Eug(1,1,i+3),e3t(1,1))
call transpose2(EUg(1,1,i+1),e1t(1,1))
call transpose2(Eug(1,1,i+2),e2t(1,1))
call transpose2(Eug(1,1,i+3),e3t(1,1))
@@
-5646,7
+5652,7
@@
C Set lprn=.true. for debugging
lprn=.false.
c lprn=.true.
etors_d=0.0D0
lprn=.false.
c lprn=.true.
etors_d=0.0D0
-c write(iout,*) "a tu??"
+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
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
diff --git
a/source/unres/src_MD-M/gradient_p.F
b/source/unres/src_MD-M/gradient_p.F
index
2c670f2
..
b5ba82a
100644
(file)
--- a/
source/unres/src_MD-M/gradient_p.F
+++ b/
source/unres/src_MD-M/gradient_p.F
@@
-292,9
+292,11
@@
c If performing constraint dynamics, add the gradients of the constraint energy
do i=1,nres-3
gloc(i,icg)=gloc(i,icg)+dugamma(i)
enddo
do i=1,nres-3
gloc(i,icg)=gloc(i,icg)+dugamma(i)
enddo
+ write(iout,*) "TU JESTEM?"
do i=1,nres-2
gloc(nphi+i,icg)=gloc(nphi+i,icg)+dutheta(i)
enddo
do i=1,nres-2
gloc(nphi+i,icg)=gloc(nphi+i,icg)+dutheta(i)
enddo
+ write(iout,*) "TU JESTEM?"
endif
#ifdef TIMING
time01=MPI_Wtime()
endif
#ifdef TIMING
time01=MPI_Wtime()
diff --git
a/source/unres/src_MD-M/int_to_cart.f
b/source/unres/src_MD-M/int_to_cart.f
index
24ce0bc
..
e178afe
100644
(file)
--- a/
source/unres/src_MD-M/int_to_cart.f
+++ b/
source/unres/src_MD-M/int_to_cart.f
@@
-24,15
+24,16
@@
c calculating dE/ddc1
& gloc(ialph(2,1)+nside,icg)*domega(j,1,2)
endif
enddo
& gloc(ialph(2,1)+nside,icg)*domega(j,1,2)
endif
enddo
+C write (iout,*) "????A CO TO??"
c Calculating the remainder of dE/ddc2
do j=1,3
gcart(j,2)=gcart(j,2)+gloc(1,icg)*dphi(j,2,4)+
& gloc(nres-2,icg)*dtheta(j,2,3)+gloc(nres-1,icg)*dtheta(j,1,4)
c Calculating the remainder of dE/ddc2
do j=1,3
gcart(j,2)=gcart(j,2)+gloc(1,icg)*dphi(j,2,4)+
& gloc(nres-2,icg)*dtheta(j,2,3)+gloc(nres-1,icg)*dtheta(j,1,4)
- if(itype(2).ne.10) then
+ if((itype(2).ne.10).and.(itype(2).ne.ntyp1)) then
gcart(j,2)=gcart(j,2)+gloc(ialph(2,1),icg)*dalpha(j,2,2)+
& gloc(ialph(2,1)+nside,icg)*domega(j,2,2)
endif
gcart(j,2)=gcart(j,2)+gloc(ialph(2,1),icg)*dalpha(j,2,2)+
& gloc(ialph(2,1)+nside,icg)*domega(j,2,2)
endif
- if(itype(3).ne.10) then
+ if((itype(3).ne.10).and.(itype(3).ne.21)) then
gcart(j,2)=gcart(j,2)+gloc(ialph(3,1),icg)*dalpha(j,1,3)+
& gloc(ialph(3,1)+nside,icg)*domega(j,1,3)
endif
gcart(j,2)=gcart(j,2)+gloc(ialph(3,1),icg)*dalpha(j,1,3)+
& gloc(ialph(3,1)+nside,icg)*domega(j,1,3)
endif
@@
-56,6
+57,7
@@
c If there are only five residues
endif
enddo
endif
endif
enddo
endif
+C write (iout,*) "Poniezej blad??",ialph(3,1),nside,ialph(4,1)
c If there are more than five residues
if(nres.gt.5) then
do i=3,nres-3
c If there are more than five residues
if(nres.gt.5) then
do i=3,nres-3
@@
-64,30
+66,31
@@
c If there are more than five residues
& +gloc(i-1,icg)*dphi(j,2,i+2)+
& gloc(i,icg)*dphi(j,1,i+3)+gloc(nres+i-4,icg)*dtheta(j,2,i+1)+
& gloc(nres+i-3,icg)*dtheta(j,1,i+2)
& +gloc(i-1,icg)*dphi(j,2,i+2)+
& gloc(i,icg)*dphi(j,1,i+3)+gloc(nres+i-4,icg)*dtheta(j,2,i+1)+
& gloc(nres+i-3,icg)*dtheta(j,1,i+2)
- if(itype(i).ne.10) then
+ if((itype(i).ne.10).and.(itype(i).ne.ntyp1)) then
gcart(j,i)=gcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,2,i)+
& gloc(ialph(i,1)+nside,icg)*domega(j,2,i)
endif
gcart(j,i)=gcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,2,i)+
& gloc(ialph(i,1)+nside,icg)*domega(j,2,i)
endif
- if(itype(i+1).ne.10) then
+ if((itype(i+1).ne.10).and.(itype(i+1).ne.ntyp1)) then
gcart(j,i)=gcart(j,i)+gloc(ialph(i+1,1),icg)*dalpha(j,1,i+1)
& +gloc(ialph(i+1,1)+nside,icg)*domega(j,1,i+1)
endif
enddo
enddo
endif
gcart(j,i)=gcart(j,i)+gloc(ialph(i+1,1),icg)*dalpha(j,1,i+1)
& +gloc(ialph(i+1,1)+nside,icg)*domega(j,1,i+1)
endif
enddo
enddo
endif
-c Setting dE/ddnres-2
+c Setting dE/ddnres-2
+ write(iout,*) "ATUCHUJ?"
if(nres.gt.5) then
do j=1,3
gcart(j,nres-2)=gcart(j,nres-2)+gloc(nres-4,icg)*
& dphi(j,3,nres-1)+gloc(nres-3,icg)*dphi(j,2,nres)
& +gloc(2*nres-6,icg)*
& dtheta(j,2,nres-1)+gloc(2*nres-5,icg)*dtheta(j,1,nres)
if(nres.gt.5) then
do j=1,3
gcart(j,nres-2)=gcart(j,nres-2)+gloc(nres-4,icg)*
& dphi(j,3,nres-1)+gloc(nres-3,icg)*dphi(j,2,nres)
& +gloc(2*nres-6,icg)*
& dtheta(j,2,nres-1)+gloc(2*nres-5,icg)*dtheta(j,1,nres)
- if(itype(nres-2).ne.10) then
+ if((itype(nres-2).ne.10).and.(itype(nres-2).ne.ntyp1)) then
gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-2,1),icg)*
& dalpha(j,2,nres-2)+gloc(ialph(nres-2,1)+nside,icg)*
& domega(j,2,nres-2)
endif
gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-2,1),icg)*
& dalpha(j,2,nres-2)+gloc(ialph(nres-2,1)+nside,icg)*
& domega(j,2,nres-2)
endif
- if(itype(nres-1).ne.10) then
+ if((itype(nres-1).ne.10).and.(itype(nres-1).ne.ntyp1)) then
gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-1,1),icg)*
& dalpha(j,1,nres-1)+gloc(ialph(nres-1,1)+nside,icg)*
& domega(j,1,nres-1)
gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-1,1),icg)*
& dalpha(j,1,nres-1)+gloc(ialph(nres-1,1)+nside,icg)*
& domega(j,1,nres-1)
@@
-98,7
+101,7
@@
c Settind dE/ddnres-1
do j=1,3
gcart(j,nres-1)=gcart(j,nres-1)+gloc(nres-3,icg)*dphi(j,3,nres)+
& gloc(2*nres-5,icg)*dtheta(j,2,nres)
do j=1,3
gcart(j,nres-1)=gcart(j,nres-1)+gloc(nres-3,icg)*dphi(j,3,nres)+
& gloc(2*nres-5,icg)*dtheta(j,2,nres)
- if(itype(nres-1).ne.10) then
+ if((itype(nres-1).ne.10).and.(itype(nres-1).ne.ntyp1)) then
gcart(j,nres-1)=gcart(j,nres-1)+gloc(ialph(nres-1,1),icg)*
& dalpha(j,2,nres-1)+gloc(ialph(nres-1,1)+nside,icg)*
& domega(j,2,nres-1)
gcart(j,nres-1)=gcart(j,nres-1)+gloc(ialph(nres-1,1),icg)*
& dalpha(j,2,nres-1)+gloc(ialph(nres-1,1)+nside,icg)*
& domega(j,2,nres-1)
@@
-106,13
+109,15
@@
c Settind dE/ddnres-1
enddo
c The side-chain vector derivatives
do i=2,nres-1
enddo
c The side-chain vector derivatives
do i=2,nres-1
- 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
gxcart(j,i)=gxcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,3,i)
& +gloc(ialph(i,1)+nside,icg)*domega(j,3,i)
enddo
endif
do j=1,3
gxcart(j,i)=gxcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,3,i)
& +gloc(ialph(i,1)+nside,icg)*domega(j,3,i)
enddo
endif
- enddo
+ enddo
+ write(iout,*) "TU DOCHODZE"
+
c----------------------------------------------------------------------
C INTERTYP=1 SC...Ca...Ca...Ca
C INTERTYP=2 Ca...Ca...Ca...SC
c----------------------------------------------------------------------
C INTERTYP=1 SC...Ca...Ca...Ca
C INTERTYP=2 Ca...Ca...Ca...SC
diff --git
a/source/unres/src_MD-M/parmread.F
b/source/unres/src_MD-M/parmread.F
index
4dd6b0a
..
9bc2d20
100644
(file)
--- a/
source/unres/src_MD-M/parmread.F
+++ b/
source/unres/src_MD-M/parmread.F
@@
-397,6
+397,7
@@
C Read torsional parameters
C
read (itorp,*,end=113,err=113) ntortyp
read (itorp,*,end=113,err=113) (itortyp(i),i=1,ntyp)
C
read (itorp,*,end=113,err=113) ntortyp
read (itorp,*,end=113,err=113) (itortyp(i),i=1,ntyp)
+ itortyp(ntyp1)=ntortyp+1
c write (iout,*) 'ntortyp',ntortyp
do i=1,ntortyp
do j=1,ntortyp
c write (iout,*) 'ntortyp',ntortyp
do i=1,ntortyp
do j=1,ntortyp
@@
-609,7
+610,7
@@
cc maxinter is maximum interaction sites
v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/
&(1+vlor3sccor(k,i,j)**2)
enddo
v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/
&(1+vlor3sccor(k,i,j)**2)
enddo
- v0sccor(i,j)=v0ijsccor
+ v0sccor(l,i,j)=v0ijsccor
enddo
enddo
enddo
enddo
enddo
enddo
diff --git
a/source/unres/src_MD-M/stochfric.F
b/source/unres/src_MD-M/stochfric.F
index
8d1cf2c
..
76aa40a
100644
(file)
--- a/
source/unres/src_MD-M/stochfric.F
+++ b/
source/unres/src_MD-M/stochfric.F
@@
-39,11
+39,7
@@
ind=ind+3
enddo
do i=nnt,nct
ind=ind+3
enddo
do i=nnt,nct
-<<<<<<< HEAD
if (itype(i).ne.10 .and. itype(i).ne.21) then
if (itype(i).ne.10 .and. itype(i).ne.21) then
-=======
- if (itype(i).ne.10) then
->>>>>>> 2acc991... Wprowadznie potencjalow SC-COR do multichain oraz ich pseudosymetrii dla
do j=1,3
d_t_work(ind+j)=d_t(j,i+nres)
enddo
do j=1,3
d_t_work(ind+j)=d_t(j,i+nres)
enddo
@@
-72,11
+68,7
@@
ind=ind+3
enddo
do i=nnt,nct
ind=ind+3
enddo
do i=nnt,nct
-<<<<<<< HEAD
if (itype(i).ne.10 .and. itype(i).ne.21) then
if (itype(i).ne.10 .and. itype(i).ne.21) then
-=======
- if (itype(i).ne.10) then
->>>>>>> 2acc991... Wprowadznie potencjalow SC-COR do multichain oraz ich pseudosymetrii dla
do j=1,3
friction(j,i+nres)=fric_work(ind+j)
enddo
do j=1,3
friction(j,i+nres)=fric_work(ind+j)
enddo
@@
-242,11
+234,7
@@
c Compute the stochastic forces acting on virtual-bond vectors.
stochforc(j,0)=ff(j)+force(j,nnt+nres)
enddo
do i=nnt,nct
stochforc(j,0)=ff(j)+force(j,nnt+nres)
enddo
do i=nnt,nct
-<<<<<<< HEAD
if (itype(i).ne.10 .and. itype(i).ne.21) then
if (itype(i).ne.10 .and. itype(i).ne.21) then
-=======
- if (itype(i).ne.10) then
->>>>>>> 2acc991... Wprowadznie potencjalow SC-COR do multichain oraz ich pseudosymetrii dla
do j=1,3
stochforc(j,i+nres)=force(j,i+nres)
enddo
do j=1,3
stochforc(j,i+nres)=force(j,i+nres)
enddo
@@
-264,11
+252,7
@@
c Compute the stochastic forces acting on virtual-bond vectors.
ind=ind+3
enddo
do i=nnt,nct
ind=ind+3
enddo
do i=nnt,nct
-<<<<<<< HEAD
if (itype(i).ne.10 .and. itype(i).ne.21) then
if (itype(i).ne.10 .and. itype(i).ne.21) then
-=======
- if (itype(i).ne.10) then
->>>>>>> 2acc991... Wprowadznie potencjalow SC-COR do multichain oraz ich pseudosymetrii dla
do j=1,3
stochforcvec(ind+j)=stochforc(j,i+nres)
enddo
do j=1,3
stochforcvec(ind+j)=stochforc(j,i+nres)
enddo