[gmx-users] Extending simulations

[Mark Abraham]

Hi,

Please start with
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

Mark

On Tue, Dec 22, 2015 at 9:10 PM masoud keramati <keramati.ma3oud at gmail.com>
wrote:

> sorry with my question
>
> is it true that for extending simulation use the following code?
>
> gmx grompp -f md.mdp -c md.gro -t md.trr -p topol.top -o md2.tpr
> gmx mdrun -deffnm md2
>
> *md.gro and md.trr is files for first run
>
> On 12/22/15, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> > On 12/21/15 7:00 PM, Soumya Lipsa Rath wrote:
> >> Dear Mark and Chandan,
> >>
> >> Thank you so much for the information. I was indeed using a wrong tpr
> >> file.
> >> I will include the -cpi state.cpt flag during the tpbconv step.
> >>
> >
> > You don't need -cpi with tpbconv, only in mdrun.
> >
> > -Justin
> >
> >> Thanks,
> >>
> >> Soumya
> >>
> >> On Mon, Dec 21, 2015 at 12:30 PM, Soumya Lipsa Rath
> >> <soumyalipsabt at gmail.com
> >>> wrote:
> >>
> >>> Dear Gromacs users,
> >>>
> >>> I am trying to extend my simulation for 200ns by using:
> >>>
> >>> tpbconv_mpi -s topol.tpr -extend 200000 -o topol2.tpr
> >>> mdrun_mpi -s topol2.tpr -cpi state.cpt -append -maxwarn 5 >&
> >>> grompp_output.log
> >>>
> >>> However, my simulation has only extended for 50ns. Am I doing something
> >>> wrong?
> >>>
> >>> Thanks,
> >>>
> >>> Soumya
> >>>
> >
> > --
> > ==================================================
> >
> > 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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