[gmx-users] Restarting Simulations

[Justin Lemkul]

On 1/4/16 6:55 PM, Soumya Lipsa Rath wrote:
> Dear Gromacs Users,
>
> I am trying to restart a simulation using the following command
>
> gmx convert-tpr -s topol.tpr -nsteps 100000000 -o topol2.tpr
>
> mdrun_mpi -s topol2.tpr -cpi state.cpt >& mdrun2_output.log
>
> But it doesn't run even a single step. The last few lines read:
>
> "starting mdrun 'Protein in water'
> 100000000 steps, 200000.0 ps (continuing from step 100000000, 200000.0 ps).
>
> Writing final coordinates.
>
> Back Off! I just backed up confout.gro to ./#confout.gro.3#"
>
> topol.tpr is my previous tpr file and I am using Gromacs 5.0.7.
> I would be obliged if I can get some suggestions.
>

The -nsteps option of convert-tpr sets the total number of steps. You've set the 
exact same number of steps that have already been run, so mdrun determines there 
is nothing for it to do other than write the final coordinates, which you 
already have.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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