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.
-Justin
Regards,
Adarsh V. K.
------------------------------
Message: 4
Date: Tue, 18 Apr 2017 08:21:56 -0400
From: Justin Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
To: gmx-us...@gromacs.org <mailto:gmx-us...@gromacs.org>
Subject: Re: [gmx-users] restart a stopped simulation after a power
failure? correct command
Message-ID: <c8f54875-63e8-3f17-50ea-c8fe506ec...@vt.edu
<mailto:c8f54875-63e8-3f17-50ea-c8fe506ec...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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