[gmx-users] extending simulations

kyungchan chae ckcumaa at umich.edu
Wed May 6 16:32:41 CEST 2009

If you want to extend your simulation, simply use the 'append' command.

: mdrun -append yes -cpi state.cpt

Extending a simulation is quite simple. However, if your trajectory file is
larger than 2GB, you are going to have a problem. I tested it a few weeks
ago and found out that the 'append' option only worked when the size of
trajectory file is smaller than 2GB. I reported this issue to Gromacs
bugzilla(#315). Please check my bug report. I really hope to share
information about this issue.

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Anna Marabotti
Sent: Wednesday, May 06, 2009 8:31 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] extending simulations

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
"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

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