t_enegrad=0.0d0
t_sdsetup=0.0d0
write (iout,'(20(1h=),a20,20(1h=))') "MD calculation started"
+ write (iout,*) "Restart frequency:",irest_freq
#ifdef MPI
tt0=MPI_Wtime()
#else
call cartout(totT)
endif
endif
- if (rstcount.eq.1000.or.itime.eq.n_timestep) then
+ if (rstcount.eq.irest_freq.or.itime.eq.n_timestep) then
open(irest2,file=rest2name,status='unknown')
write(irest2,*) totT,EK,potE,totE,t_bath
- do i=1,2*nres
+ do i=0,2*nres-1
write (irest2,'(3e15.5)') (d_t(j,i),j=1,3)
enddo
- do i=1,2*nres
+ do i=0,2*nres-1
write (irest2,'(3e15.5)') (dc(j,i),j=1,3)
enddo
close(irest2)
& ' End of MD calculation '
#ifdef TIMING_ENE
write (iout,*) "time for etotal",t_etotal," elong",t_elong,
- & " eshort",t_eshort
+ & " eshort",t_eshort," list",time_list
write (iout,*) "time_fric",time_fric," time_stoch",time_stoch,
& " time_fricmatmult",time_fricmatmult," time_fsample ",
& time_fsample
call zerograd
call etotal(potEcomp)
! AL 4/17/17: Reduce the steps if NaNs occurred.
- if (potEcomp(0).gt.0.99e20 .or. isnan(potEcomp(0)).gt.0) then
+ if (potEcomp(0).gt.0.99e20 .or. isnan(potEcomp(0))) then
d_time=d_time/2
cycle
endif
integer iran_num
double precision etot
logical fail
+ integer i_start_models(0:nodes-1)
+ double precision potEcomp_long(0:Max_Ene)
write (iout,*) "init_MD INDPDB",indpdb
d_time0=d_time
c write(iout,*) "d_time", d_time
if (me.eq.king)
& inquire(file=mremd_rst_name,exist=file_exist)
#ifdef MPI
- write (*,*) me," Before broadcast: file_exist",file_exist
+c write (*,*) me," Before broadcast: file_exist",file_exist
call MPI_Bcast(file_exist,1,MPI_LOGICAL,king,CG_COMM,
& IERR)
- write (*,*) me," After broadcast: file_exist",file_exist
+c write (*,*) me," After broadcast: file_exist",file_exist
c inquire(file=mremd_rst_name,exist=file_exist)
#endif
if(me.eq.king.or..not.out1file)
if(me.eq.king.or..not.out1file)then
write (iout,*) "Initial velocities"
do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),
+ write (iout,'(i7,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),
& (d_t(j,i+nres),j=1,3)
enddo
endif
call flush(iout)
endif
endif
- write (iout,*) "init_MD before initial structure REST ",rest
+c write (iout,*) "init_MD before initial structure REST ",rest
+ if(start_from_model .and. (me.eq.king .or. .not. out1file))
+ & write(iout,*) 'START_FROM_MODELS is ON'
+ if(start_from_model .and. rest) then
+ if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*)
+ & 'START_FROM_MODELS is OFF because the run is restarted'
+ write(iout,*) 'Remove restart keyword from input'
+ endif
+ endif
+c write (iout,*) "rest ",rest," start_from_model",start_from_model,
+c & " nmodel_start",nmodel_start," preminim",preminim
if (.not.rest) then
122 continue
if (iranconf.ne.0) then
else if (preminim) then
if (start_from_model) then
n_model_try=0
- do while (fail .and. n_model_try.lt.constr_homology)
+ fail=.true.
+ list_model_try=0
+ do while (fail .and. n_model_try.lt.nmodel_start)
+ write (iout,*) "n_model_try",n_model_try
do
- i_model=iran_num(1,constr_homology)
+ i_model=iran_num(1,nmodel_start)
do k=1,n_model_try
if (i_model.eq.list_model_try(k)) exit
enddo
enddo
n_model_try=n_model_try+1
list_model_try(n_model_try)=i_model
- write (iout,*) 'starting from model ',i_model
+ if (me.eq.king .or. .not. out1file)
+ & write (iout,*) 'Trying to start from model ',
+ & pdbfiles_chomo(i_model)(:ilen(pdbfiles_chomo(i_model)))
do i=1,2*nres
do j=1,3
c(j,i)=chomo(j,i,i_model)
enddo
call int_from_cart(.true.,.false.)
call sc_loc_geom(.false.)
+ dc(:,0)=c(:,1)
do i=1,nres-1
do j=1,3
dc(j,i)=c(j,i+1)-c(j,i)
cycle
endif
endif
-#ifdef SEARCHSC
if (me.eq.king.or..not.out1file) then
write (iout,*) "Energies after removing overlaps"
call etotal(energia(0))
call enerprint(energia(0))
endif
+#ifdef SEARCHSC
! Search for better SC rotamers if requested
if (searchsc) then
call sc_move(2,nres-1,10,1d10,nft_sc,etot)
call etotal(energia(0))
#endif
enddo
- if (n_model_try.gt.constr_homology) then
+ call MPI_Gather(i_model,1,MPI_INTEGER,i_start_models(0),
+ & 1,MPI_INTEGER,king,CG_COMM,IERROR)
+ if (n_model_try.gt.nmodel_start .and.
+ & (me.eq.king .or. out1file)) then
write (iout,*)
& "All models have irreparable overlaps. Trying randoms starts."
iranconf=1
+ i_model=nmodel_start+1
goto 122
endif
+ else
+! Remove SC overlaps if requested
+ if (overlapsc) then
+ write (iout,*) 'Calling OVERLAP_SC'
+ call overlap_sc(fail)
+ if (fail) then
+ write (iout,*)
+ & "Failed to remove overlap"
+ endif
+ endif
+ if (me.eq.king.or..not.out1file) then
+ write (iout,*) "Energies after removing overlaps"
+ call etotal(energia(0))
+ call enerprint(energia(0))
+ endif
endif
C 8/22/17 AL Minimize initial structure
if (dccart) then
#endif
endif
endif
+ if (nmodel_start.gt.0 .and. me.eq.king) then
+ write (iout,'(a)') "Task Starting model"
+ do i=0,nodes-1
+ if (i_start_models(i).gt.nmodel_start) then
+ write (iout,'(i4,2x,a)') i,"RANDOM STRUCTURE"
+ else
+ write(iout,'(i4,2x,a)')i,pdbfiles_chomo(i_start_models(i))
+ & (:ilen(pdbfiles_chomo(i_start_models(i))))
+ endif
+ enddo
+ endif
endif ! .not. rest
call chainbuild_cart
call kinetic(EK)
call verlet_bath
endif
kinetic_T=2.0d0/(dimen3*Rb)*EK
+ write (iout,*) "Initial kinetic energy",EK," kinetic T",kinetic_T
if(me.eq.king.or..not.out1file)then
call cartprint
call intout
call zerograd
call etotal(potEcomp)
if (large) call enerprint(potEcomp)
+ if (RESPA) call etotal_long(potEcomp_long)
#ifdef TIMING_ENE
#ifdef MPI
t_etotal=t_etotal+MPI_Wtime()-tt0
call cartgrad
call lagrangian
call max_accel
- if (amax*d_time .gt. dvmax) then
+ if (amax*d_time .gt. dvmax .and. .not. respa) then
d_time=d_time*dvmax/amax
if(me.eq.king.or..not.out1file) write (iout,*)
& "Time step reduced to",d_time,