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

[James Starlight]

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 ?


James

2012/9/13 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 9/13/12 9:56 AM, James Starlight wrote:
>>
>> Justin,
>>
>> I've used
>>
>>
>> grompp -f md_sd.mdp -c start.gro -t incomplete.cpt -p topol.top -o
>> incomplete.tpr
>> 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?
>>
>
> You shouldn't be invoking grompp at all.
>
> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#Version_4.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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