[gmx-users] extending simulations
zhlrui at 163.com
Wed May 6 15:33:20 CEST 2009
You can use the mdrun command:
How to restart a crashed run. The mdrun program now uses a very handy checkpointing feature.
Restarting crashed runs is easy with mdrun.
mdrun -s prev.tpr -f prev.trr -e prev.edr -o prev.trr –g prev.log –cpi -append
在2009-05-06，"Anna Marabotti" <anna.marabotti at isa.cnr.it> 写道：
>I'd need to have a clarification about how to extend a simulation made using GROMACS 4 that has been
>interrupted on a system due to walltime expiration. On the Wiki section I see:
>"A simulation that has completed is extended using tpbconv, mdrun and checkpoint files (.cpt). A simulation
>that has terminated, but not completed, due to e.g. the queue time ending, or better: the use of the -maxh
>option of mdrun, can be continued without tpbconv. First the number of steps or time has to be changed in the
>.tpr file, then the simulation is continued from the last checkpoint with mdrun. This will produce a binary
>identical simulation that will be the same as it a continuous run was made.
>tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
>mdrun -s next.tpr -cpi previous.cpt"
>If I understand well, the procedure using tpbconv should be applied only if I have finished my previous run
>of, say, 10 ns, and I want to extend it to 20 ns. ONLY in this case I have to use tpbconv and then mdrun. On
>the contrary, if my run of 10 ns has been interrupted e.g. at 7 ns, the only command I should provide is:
>mdrun -s previous.tpr -cpi previous.cpt
>without modifying the previous.tpr file.
>Could you please confirm me about this point?
>Many thanks and best regards
>Anna Marabotti, Ph.D.
>Laboratory of Bioinformatics and Computational Biology
>Institute of Food Science, CNR
>Via Roma 64
>83100 Avellino (Italy)
>Phone: +39 0825 299651
>Fax: +39 0825 781585
>E-mail: amarabotti at isa.cnr.it
>Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
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