X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2FMD.f90;h=3725902b446821db4a162c33a10183125febf9ca;hb=4fa6ed0fa1ee37552df6064fe60a73f218c101ca;hp=c378ece42815f7cfb496d30e53769a760bf39e23;hpb=bd02e13419b372715884200b98a58b48e1407f62;p=unres4.git

diff --git a/source/unres/MD.f90 b/source/unres/MD.f90
index c378ece..3725902 100644
--- a/source/unres/MD.f90
+++ b/source/unres/MD.f90
@@ -98,33 +98,33 @@
 !el      integer maxamino,maxnuc,maxbnd
 !el      integer maxang,maxtors,maxpi
 !el      integer maxpib,maxpit
-      integer :: maxatm	!=2*nres	!maxres2 maxres2=2*maxres
-      integer,parameter :: maxval=8
-      integer,parameter :: maxgrp=1000
-      integer,parameter :: maxtyp=3000
-      integer,parameter :: maxclass=500
-      integer,parameter :: maxkey=10000
-      integer,parameter :: maxrot=1000
-      integer,parameter :: maxopt=1000
-      integer,parameter :: maxhess=1000000
-      integer :: maxlight	!=8*maxatm
-      integer,parameter :: maxvib=1000
-      integer,parameter :: maxgeo=1000
-      integer,parameter :: maxcell=10000
-      integer,parameter :: maxring=10000
-      integer,parameter :: maxfix=10000
-      integer,parameter :: maxbio=10000
-      integer,parameter :: maxamino=31
-      integer,parameter :: maxnuc=12
-      integer :: maxbnd		!=2*maxatm
-      integer :: maxang		!=3*maxatm
-      integer :: maxtors	!=4*maxatm
-      integer,parameter :: maxpi=100
-      integer,parameter :: maxpib=2*maxpi
-      integer,parameter :: maxpit=4*maxpi
+!      integer :: maxatm	!=2*nres	!maxres2 maxres2=2*maxres
+!      integer,parameter :: maxval=8
+!      integer,parameter :: maxgrp=1000
+!      integer,parameter :: maxtyp=3000
+!      integer,parameter :: maxclass=500
+!      integer,parameter :: maxkey=10000
+!      integer,parameter :: maxrot=1000
+!      integer,parameter :: maxopt=1000
+!      integer,parameter :: maxhess=1000000
+!      integer :: maxlight	!=8*maxatm
+!      integer,parameter :: maxvib=1000
+!      integer,parameter :: maxgeo=1000
+!      integer,parameter :: maxcell=10000
+!      integer,parameter :: maxring=10000
+!      integer,parameter :: maxfix=10000
+!      integer,parameter :: maxbio=10000
+!      integer,parameter :: maxamino=31
+!      integer,parameter :: maxnuc=12
+!      integer :: maxbnd		!=2*maxatm
+!      integer :: maxang		!=3*maxatm
+!      integer :: maxtors	!=4*maxatm
+!      integer,parameter :: maxpi=100
+!      integer,parameter :: maxpib=2*maxpi
+!      integer,parameter :: maxpit=4*maxpi
 !-----------------------------------------------------------------------------
 ! Maximum number of seed
-      integer,parameter :: max_seed=1
+!      integer,parameter :: max_seed=1
 !-----------------------------------------------------------------------------
       real(kind=8),dimension(:),allocatable :: stochforcvec !(MAXRES6) maxres6=6*maxres
 !      common /stochcalc/ stochforcvec
@@ -548,6 +548,7 @@
       potE=potEcomp(0)-potEcomp(20)
       call cartgrad
       totT=totT+d_time
+      totTafm=totT
 !  Calculate the kinetic and total energy and the kinetic temperature
       call kinetic(EK)
 #ifdef MPI
@@ -1001,6 +1002,7 @@
         if (rstcount.eq.1000.or.itime.eq.n_timestep) then
            open(irest2,file=rest2name,status='unknown')
            write(irest2,*) totT,EK,potE,totE,t_bath
+        totTafm=totT 
 ! AL 4/17/17: Now writing d_t(0,:) too
            do i=0,2*nres
             write (irest2,'(3e15.5)') (d_t(j,i),j=1,3)
@@ -1287,6 +1289,7 @@
           endif 	    	    
           if (rattle) call rattle2
           totT=totT+d_time
+        totTafm=totT
           if (d_time.ne.d_time0) then
             d_time=d_time0
 #ifndef   LANG0
@@ -1726,6 +1729,7 @@
       potE=potEcomp(0)-potEcomp(20)
 !      potE=energia_short(0)+energia_long(0)
       totT=totT+d_time
+        totTafm=totT
 ! Calculate the kinetic and the total energy and the kinetic temperature
       call kinetic(EK)
       totE=EK+potE
@@ -2403,6 +2407,7 @@
         endif
         call random_vel
         totT=0.0d0
+        totTafm=totT
        endif
       else
 ! Generate initial velocities
@@ -2410,6 +2415,7 @@
          write(iout,*) "Initial velocities randomly generated"
         call random_vel
         totT=0.0d0
+        totTafm=totT
       endif
 !      rest2name = prefix(:ilen(prefix))//'.rst'
       if(me.eq.king.or..not.out1file)then
@@ -2435,7 +2441,7 @@
        write (iout,*) "vcm right after adjustment:"
        write (iout,*) (vcm(j),j=1,3) 
       endif
-      if (.not.rest) then	  	
+      if ((.not.rest).and.(indpdb.eq.0)) then	  	
          call chainbuild
          if(iranconf.ne.0) then
           if (overlapsc) then 
@@ -4481,7 +4487,7 @@
 !el      common /przechowalnia/ GGinv,gdc,Cmat,nbond
 !el      common /przechowalnia/ nbond
       integer :: max_rattle = 5
-      logical :: lprn = .true., lprn1 = .true., not_done
+      logical :: lprn = .false., lprn1 = .false., not_done
       real(kind=8) :: tol_rattle = 1.0d-5
       integer :: nres2
       nres2=2*nres
@@ -5505,11 +5511,11 @@
       logical :: omit(maxarc)
 !
 !      include 'sizes.i'
-      maxatm = 2*nres	!maxres2 maxres2=2*maxres
-      maxlight = 8*maxatm
-      maxbnd = 2*maxatm
-      maxang = 3*maxatm
-      maxtors = 4*maxatm
+!      maxatm = 2*nres	!maxres2 maxres2=2*maxres
+!      maxlight = 8*maxatm
+!      maxbnd = 2*maxatm
+!      maxang = 3*maxatm
+!      maxtors = 4*maxatm
 !
 !     zero out the surface area for the sphere of interest
 !