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Hi,<br><br>You have explicitly specified md_0_1_prev.cpt instead of md_0_1.cpt as checkpoint.<br>So you are using the previous checkpoint instead of the last one.<br>The final result will be fine, but you will be redoing part of a simulation<br>that you had already done.<br><br>Berk<br><br>> Date: Mon, 14 Sep 2009 14:59:54 +0200<br>> From: Stephane.Abel@cea.fr<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Continuation a run with checkpoint issue<br>> <br>> Hi gromacs users<br>> <br>> I would like to continue a run up 3000 ps (with a preceding MD performed <br>> during a 1ns) on a cluser with 8 CPU<br>> <br>> Here the commands i used<br>> <br>> Run 1: during 1 ns in NVT ensemble<br>> <br>> grompp_mpi -f md.mdp -c nvt.gro -t npt.trr -p topol.top -o md_0_1.tpr<br>> <br>> /usr/pbs/bin/mpiexec /scratch/taulier01/gromacs-4.0.5/bin/mdrun_mpi <br>> -deffnm md_0_1 -v<br>> <br>> Run 2 : continuation of the run 1 until 3 ns (command adapted from the <br>> wiki page http://oldwiki.gromacs.org/index.php/Extending_Simulations)<br>> <br>> tpbconv_mpi -s md_0_1.tpr -extend 2000 -o md_1_3.tpr<br>> /usr/pbs/bin/mpiexec /scratch/taulier01/gromacs-4.0.5/bin/mdrun_mpi -s <br>> md_1_3.tpr -cpi md_0_1_prev.cpt<br>> <br>> The job starts well but when i take a look of the run 2 log file the <br>> first step is not 1000 ps (as i would expect) but<br>> <br>> Step Time Lambda<br>> 463000 926.00006 0.00000<br>> <br>> It is normal ? Since i am a new user of gromacs, i don't know if the previous commands are corrects. <br>> <br>> Any advice will be appreciate. <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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