Hello, 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, Alexander > 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-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Anna Marabotti >> Sent: Wednesday, May 06, 2009 8:31 AM >> To: gmx-users@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: amarabo...@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" >> >> _______________________________________________ >> gmx-users mailing list gmx-us...@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the www interface >> or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
