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

James Starlight jmsstarlight at gmail.com
Thu Sep 13 15:56:53 CEST 2012


I've used

grompp -f md_sd.mdp -c start.gro -t incomplete.cpt -p topol.top -o
mpiexec -np 48 mdrun_mpi.openmpi -v -deffnm incomplete -append

where incomplete.cpt was checkpoint from previous run and -o
incomplete.tpr was the name for new trajectory (in that case its equal
to the name of old trajectory )

that produce new .trr .edr and other files and back up old ( e.g crete
#incomplete.trr etc) ones instead of continuation of the existing (
incomplete ) trajectory

What I've done wrong?

2012/9/13, Justin Lemkul <jalemkul at vt.edu>:
> On 9/13/12 1:12 AM, James Starlight wrote:
>> Dear Gromacs Users!
>> I'm looking for possible way to resume trajectory calculations after
>> that calculations have been stoped.
>> Typically in such cases I start new task using cpt file from
>> incomplete run. This produce new trajectory which start from the last
>> frame of previous run. After that I have to merge both files.
>> Is there any way to go on sinulation in the existed files from the
>> last frame of incomplete run without creating of new ones?
> You can only continue from the last frame if you have a checkpoint file that
> corresponds to that frame.  Use of the -append flag with mdrun will append
> to
> existing files rather than creating new ones.  This should be default
> behavior
> in Gromacs 4.5.x.
> -Justin
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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