[gmx-users] extending simulations

Alexander Itkin itkin at umich.edu
Fri May 22 22:51:29 CEST 2009


I am having a similar issue. When using Gromacs version 4.0.4 and
running mdrun with the -append flag on a traj.trr file over 2GB I get
an error stating "Truncation of traj.trr file failed". However, when I
use version 4.0.2 it seems to append fine even with very large files.
Any ideas as to what could be the cause of this? In both versions I
used single precision.

Any info would be greatly appereciated.

Thank you,

> kyungchan chae wrote:
>> 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
>> 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
>> ______________________________________________
>> 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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