[gmx-users] Extending simulation with modifing .mdp file

Justin Lemkul jalemkul at vt.edu
Fri Aug 14 13:31:20 CEST 2015

On 8/13/15 10:03 AM, Asmaa El khodary wrote:
> Hi.
> I want to extend a simulation by 50000 ps, but also I want to change some
> parameters in the old mdp file, so I type (run.mdp is the modified file) :
> grompp_mpi -f run.mdp -c run_50.tpr -o run1_50.tpr
> tpbconv_mpi -s run_50.tpr -extend 50000 -o run1_50.tpr
> mpirun -np 60 mdrun_mpi -v -deffnm run1_50 -cpi run_50.cpt -append
> Is this correct?

You don't need both grompp and tpbconv.

> Another question. I'm using nose-hoover thermostat and Parrinello-Rahman
> barostat in production run . Is using md integrator convenient?

Pretty standard.



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


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