[gmx-users] Re: Extending a simulation

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 18 01:38:27 CEST 2012

Shyno Mathew wrote:
> Hello Justin,
> Thanks for your reply.
> Now I have another question about appending the data to previous files.
> I am running the simulation on a cluster and this is how the main line 
> on my job script looks like:
> mpiexec -n 10 mdrun_dp_mpich2 -s equil_02.tpr -cpi equil_01.cpt -append yes
> Initially i didn't specify the append option as appending is the default 
> behavior as of version 4.5
> I am using version 4.5.5, (gromacs/4.5.5-dp-mpich2/bin/mdrun_dp)
> Even after specifying the append option, I can see the following new 
> files are being created,
> traj.trr, traj.xtc, ener.edr, md.log.

They should.  In the absence of -deffnm, those are the default names used for 
output files.  If you have those files present from a previous run, mdrun will 
append the new content.  If those files are not present, I believe mdrun should 
create them as new files, not appended to existing files.



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


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