[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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