triss; AFM; Lorentz restrains included -debug might be on

[unres4.git] / source / unres / MD.f90

diff --git a/source/unres/MD.f90 b/source/unres/MD.f90
index 36124aa..3725902 100644 (file)
--- a/source/unres/MD.f90
+++ b/source/unres/MD.f90
@@ -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