[gmx-users] Restarting a simulation when checkpoint files are corrupted

David Dotson dldotson at asu.edu
Fri Mar 17 18:00:01 CET 2017


I have a simulation that has been running for a long time, with many trajectory segments (counting up to about 190). One of the segments ran on a cluster that experienced a filesystem outage such that some of the files for that run were corrupted, including its checkpoint files (both the *.cpt and *_prev.cpt, somehow). Since I only have checkpoint files for the most recent run, I need to do something like a manual restart.

I'm aware I can do this with `gmx convert-tpr` using an existing TPR and the most recent uncorrupted TRR and EDR file, but starting a run from this restarts counting for the output files from `0001`. Is there some way to make counting start from another value (like `0191`)?

If not, I can work around this I think by concatenating the existing parts and moving forward with restarted counting, but being able to do this would be the cleanest solution for me in this particular case to maintain some consistency with other runs.



David L. Dotson * david.dotson at asu.edu
Beckstein Lab
Center for Biological Physics
Arizona State University


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