[gmx-users] Continuation a run with checkpoint issue
Stephane Abel
Stephane.Abel at cea.fr
Mon Sep 14 14:59:54 CEST 2009
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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