[gmx-users] extending simulations

Anna Marabotti anna.marabotti at isa.cnr.it
Wed May 6 14:30:37 CEST 2009

Dear all,
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
Skype: annam1972
E-mail: amarabotti at isa.cnr.it
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
"If you think you are too small to make a difference, try sleeping with a mosquito"

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