[gmx-users] Resuming of calculation from last *.cpt

Justin Lemkul jalemkul at vt.edu
Sat Sep 15 16:06:43 CEST 2012

On 9/15/12 10:03 AM, James Starlight wrote:
> Justin,
> In accordance to the manual I've re-launched my simulation by the command
> mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial  -cpi md_initial  -append
> where md_initial is the name of the files from the run which I want to continue.
> As the result this produce new files with the default names traj.trr
> ener.edr etc. In those files the trajectory have been calculated from
> the last frame of the md_initial.cpt file. So as the result I've
> obtain again 2 set of output files ( from old and new runs). IS it
> possible to continue the calculations and save output within the
> existing files (md_initial) without creation of new ones ?

The names of the files produced depend on what is stored in the .cpt file. 
mdrun will only append to files with those names.  I don't have a clear picture 
of what you've done so it's impossible to say whether or not this is the 
expected outcome, but the checkpointing feature is very robust so I suspect it 
is.  Were all of  your file names originally called md_initial?  If you've 
re-named them, the appending will fail for that very reason.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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