[gmx-users] Extending simulations

[Maryam Kowsar]

Hi

I think it should be like this:
tpbconv -s previous.tpr -extend timetoextendby -o new.tpr
mdrun -s new.tpr -cpi previous.cpt


On Tue, Dec 22, 2015 at 2:07 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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