[gmx-users] Restarting a crashed MD run
bmmothan at ucalgary.ca
bmmothan at ucalgary.ca
Tue May 1 21:57:39 CEST 2007
Thank you. I will save some energies and velocities in future simulations.
but in this email, my job was not crashed..I terminated it and it wrote
the last velocities and when i wanted to contiune it using pbdconj, it
said it will finish the simulation from the time I terminated it.
so is this accurate enough to finish it?
> Is it not better to save energies also once in a while along with the
> velocities to make sure the restart of a crashed simulation is
> On 5/1/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>> bmmothan at ucalgary.ca wrote:
>> > sorry to ask again, I hope this is my last question about this.
>> > since I know now that the restarted run I did started from 0 time. I
>> > killed the job and it wrote velocity for the last frame. So since i
>> knew i
>> > have to contiune this run that I just killed, I used tpbconj and it
>> > a new tpr file and it said it will restart it from the time I killed
>> > job ( half the simulation). SO i think I am set now to continue the
>> > simulation this way.
>> > Thank u
>> If your simulation crashes without saving to the trr you'll have to
>> restart from your last tpr again.
>> It would be more systematic to save velocities every once in a while,
>> depending on how much time you can afford to lose.
>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>> phone: 46 18 471 4205 fax: 46 18 511 755
>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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> Viswanadham Sridhara,
> Research Assistant,
> Old Dominion University,
> Norfolk, Va-23529.
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