[gmx-users] Restart a stopped simulation after a power failure? correct command (Justin Lemkul) : gromacs.org_gmx-users Digest, Vol 156, Issue 81
jalemkul at vt.edu
Thu Apr 20 13:59:33 CEST 2017
Please keep the discussion on the mailing list.
On 4/20/17 3:42 AM, Adarsh V. K. wrote:
> Dear Dr. Justin,
> Are you specifically asking about frames ?... It is 650 -> 6500 ps (not appended
> the log file after the restart from 6500ps to 8000ps).
> 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?
Your command is fine. You still haven't done what I asked, which was to
investigate the contents of your files (e.g. trajectory, energy) with gmx check
to see what it tells you about their contents. You assert that data are missing
but you have provided no evidence of that.
> Adarsh V. K.
> Message: 4
> Date: Tue, 18 Apr 2017 08:21:56 -0400
> From: Justin Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> To: gmx-users at gromacs.org <mailto: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
> <mailto: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 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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