[gmx-users] extending simulations

Justin A. Lemkul jalemkul at vt.edu
Wed May 6 15:31:44 CEST 2009

Anna Marabotti wrote:
> 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

Yes.  And the -append option, if you want to continue writing to the same output 
files, without having to use trjcat/eneconv later.


> without modifying the previous.tpr file.
> Could you please confirm me about this point?
> Many thanks and best regards
> Anna
> ______________________________________________
> 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
> ____________________________________________________
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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