[gmx-users] Continuation a run with checkpoint issue
gmx3 at hotmail.com
Mon Sep 14 16:24:20 CEST 2009
You have explicitly specified md_0_1_prev.cpt instead of md_0_1.cpt as checkpoint.
So you are using the previous checkpoint instead of the last one.
The final result will be fine, but you will be redoing part of a simulation
that you had already done.
> Date: Mon, 14 Sep 2009 14:59:54 +0200
> From: Stephane.Abel at cea.fr
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Continuation a run with checkpoint issue
> Hi gromacs users
> I would like to continue a run up 3000 ps (with a preceding MD performed
> during a 1ns) on a cluser with 8 CPU
> Here the commands i used
> Run 1: during 1 ns in NVT ensemble
> grompp_mpi -f md.mdp -c nvt.gro -t npt.trr -p topol.top -o md_0_1.tpr
> /usr/pbs/bin/mpiexec /scratch/taulier01/gromacs-4.0.5/bin/mdrun_mpi
> -deffnm md_0_1 -v
> Run 2 : continuation of the run 1 until 3 ns (command adapted from the
> wiki page http://oldwiki.gromacs.org/index.php/Extending_Simulations)
> tpbconv_mpi -s md_0_1.tpr -extend 2000 -o md_1_3.tpr
> /usr/pbs/bin/mpiexec /scratch/taulier01/gromacs-4.0.5/bin/mdrun_mpi -s
> md_1_3.tpr -cpi md_0_1_prev.cpt
> The job starts well but when i take a look of the run 2 log file the
> first step is not 1000 ps (as i would expect) but
> Step Time Lambda
> 463000 926.00006 0.00000
> It is normal ? Since i am a new user of gromacs, i don't know if the previous commands are corrects.
> Any advice will be appreciate.
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