[gmx-users] Extend the simulation

[Mark Abraham]

Hi,

Please do exactly what Justin has suggested twice :-)

Mark

On Sun, 21 Feb 2016 02:21 Elsaid Younes <elkhot at gmail.com> wrote:

> Ok, How can I use md_0_1.tpr instead of topol.tpr
>
> /Elsaid
>
> On Sun, Feb 21, 2016 at 2:59 AM, Elsaid Younes <elkhot at gmail.com> wrote:
>
> > Hi,
> >
> > The mdrun I did was gmx mdrun -deffnm md_0_1
> > I write the command
> >  mdrun -cpi md_0_1_prev.cpt -append
> >  I tried to use -noappend, but still doesn't work.
> >
> > /Elsaid
> >
> > On Sun, Feb 21, 2016 at 2:43 AM, Elsaid Younes <elkhot at gmail.com> wrote:
> >
> >> Still asks for topol.tpr? Can I have that file
> >>
> >>
> >> /Elsaid
> >> On 2/20/16 6:49 PM, Elsaid Younes wrote:
> >> >* Hi,
> >> *>>>* If I have this file md_0_1_prev.cpt What is the text exactly? It
> asks
> >> *>* for topol.tpr
> >> *
> >> I gave you the command-line options that are new to the mdrun command
> line.  Run
> >> whatever mdrun you did before, but add -cpi -append.  Doing this is a
> routine
> >> task, covered on the website and in half a million posts in the archive
> (Google
> >> is your friend).
> >>
> >> -Justin
> >>
> >> >* On 2/20/16 5:32 PM, Elsaid wrote:
> >> *>>* * The simulation has the time,  which is time of the wanted
> simulation. But the
> >> *>* *>* job was killed by the server.
> >> *>* *
> >> *>* If the simulation terminated prior to completion, you don't need to
> operate on
> >> *>* the .tpr file at all.  Just continue from the last checkpoint
> >> *>>* mdrun -cpi -append
> >> *>>* -Justin*
> >>
> >>
> >> On Sun, Feb 21, 2016 at 1:49 AM, Elsaid Younes <elkhot at gmail.com>
> wrote:
> >>
> >>> Hi,
> >>>
> >>>
> >>> If I have this file md_0_1_prev.cpt What is the text exactly? It asks
> for topol.tpr
> >>> On 2/20/16 5:32 PM, Elsaid wrote:
> >>> >* The simulation has the time,  which is time of the wanted
> simulation. But the
> >>> *>* job was killed by the server.
> >>> *
> >>> If the simulation terminated prior to completion, you don't need to
> operate on
> >>> the .tpr file at all.  Just continue from the last checkpoint
> >>>
> >>> mdrun -cpi -append
> >>>
> >>> -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 <
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> |
> (410) 706-7441http://mackerell.umaryland.edu/~jalemkul
> >>>
> >>>
> >>>
> >>> On Sun, Feb 21, 2016 at 12:32 AM, Elsaid <elkhot at gmail.com> wrote:
> >>>
> >>>> The simulation has the time,  which is time of the wanted simulation.
> >>>> But the job was killed by the server.
> >>>> /Elsaid
> >>>>
> >>>
> >>>
> >>
> >
> --
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