[gmx-users] Continuation a run with checkpoint issue

[Justin A. Lemkul]

Stephane Abel wrote:
> 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
> 

Why are you using the previous checkpoint?  mdrun backs up the .cpt file when it 
writes a new one.  You should have md_0_1.cpt, which corresponds to the end of 
your simulation; it should be passed to mdrun to start the next segment of 
simulation time.

-Justin

> 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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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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