[gmx-users] restart a stopped simulation after a power failure? correct command (Justin Lemkul) : gromacs.org_gmx-users Digest, Vol 156, Issue 81

[Mark Abraham]

Hi,

The log file tells you where the restart wrote its output. You can confirm
that by looking at the contents of your output directory. Probably you
changed something between the two commands (eg your use of -deffnm) and
will now need to manually concatenate some files. Justin asked you to use
gmx check for a reason.

Mark

On Wed, 19 Apr 2017 06:34 Adarsh V. K. <adarsh_p130085bt at nitc.ac.in> wrote:

> >
> > Dear Dr. Justin,
> >
>
> I have checked the log files. It appeared that no details appended after
> restarting simulation (after power failure at 6.5 ns), Even Though the
> 'terminal' Ubuntu 16.04 shows that the simulation successfully restarted
> from 6.5 ns (used 8 processor cores + Graphics card GTX 780Ti) and
> completed the entire 8 ns simulation...!!.
>
> I used the command (gromacs 5.1.4),  mdrun -s md.tpr -cpi state.cpt
>
> I also tried, mdrun -s md.tpr -cpi state.cpt -append
>
> Is it any modification required in command?
>
> Regards,
> Adarsh V. K.
>
> > ------------------------------
> >
> > Message: 4
> > Date: Tue, 18 Apr 2017 08:21:56 -0400
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] restart a stopped simulation after a power
> >         failure? correct command
> > Message-ID: <c8f54875-63e8-3f17-50ea-c8fe506ec387 at vt.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > On 4/18/17 1:21 AM, Adarsh V. K. wrote:
> > > Dear all,
> > >
> > > I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
> > > stopped simulation after a power failure?
> > >
> > > I used the following command to restart the stopped simulation at 6.5
> ns.
> > >
> > > *mdrun -s md.tpr -cpi state.cpt*
> > >
> > > Even Though the simulation appeared to be restarted successfully and
> > > completed required 8.0 ns, the data analysis showed that the simulation
> > was
> > > stopped at 6.5ns...!!!. ( Not re-started from 6.5 ns and continued till
> > 8.0
> > > ns.)
> > >
> >
> > What does gmx check tell you about your files, e.g. how many frames does
> > it find
> > in the trajectory?  Does the .log file or stderr/stdout give any clues
> > about how
> > appending was treated?
> >
> > -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
> >
> > ==================================================
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>