[gmx-users] Restart a simulation from a power source failure
Justin A. Lemkul
jalemkul at vt.edu
Mon Aug 8 23:10:12 CEST 2011
Luís Pereira wrote:
> Hi Justin,
> Thank you for your quick answer.
> All the files are in the working directory but have different names,
> e.g., the .trr is not traj.trr but 7fboh3.trr, and so on.
If you do not supply filenames, then the defaults are assumed. This is true of
all Gromacs programs.
> I've backed up the working directory, run gromacs with all output file
> names written in command line and now everything is working fine:
> 1000000 steps, 1000.0 ps (continuing from step 878000, 878.0 ps).
> Well, i'll have to wait to see if the final results are ok.
They should be, provided the command issued is correct.
> On 8 August 2011 21:47, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> Luís Pereira wrote:
> Hi all,
> I'm trying to restart a simulation from a power source failure,
> but mdrun complains about a missing .trr file:
> Program mdrun, VERSION 4.0.7
> Source code file: ../../../../src/gmxlib/gmxfio.__c, line: 737
> Can not open file:
> The manual says that there is no need to supply more information
> mdrun -s topol.tpr -cpi state.cpt -append
> Do I have to write all the output files in the above command
> line? Or there was something wrong when gromacs wrote the
> checkpoint file?
> If you're appending, then all the expected files must be present in
> the working directory, unmodified. It appears that this is not the
> case, as traj.trr is missing. You can always use -noappend and
> concatenate any relevant output later.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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