VMD-L Mailing List

From: Sefcikova, Jana (j.sefcikova_at_northeastern.edu)
Date: Tue Apr 30 2024 - 17:41:39 CDT

Hi Giacomo,

If I understand correctly, it is NOT possible to restart “the next job” directly from QwikMD using “filename.qwikmd file”, right?

Best,
Jana

From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Tuesday, April 30, 2024 5:10 PM
To: Sefcikova, Jana <j.sefcikova_at_northeastern.edu>
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: restarting calculations anytime within Equilibration and MD simulations steps in QwikMD

Hi Jana,

How do I submit “the next job”?

Handling dependent jobs depends on the type of scheduler that is being used in the cluster. The most common is Slurm, where you would add a --depend flag to sbatch: https://urldefense.com/v3/__https://slurm.schedmd.com/sbatch.html__;!!DZ3fjg!5LcFu8DlUgMLPNGCXXkRfLXBN7VHdUXWUbwKtgkF6AeUTw-C6iiOHKdE1hpyTY6HzSj-1hO5Usrl0OCIggim1uYkA6Cpcw$ But the specifics will be decided by your cluster admins: documenting the batch system is part of their core duties.

Regards
Giacomo

Thanks,
Jana

Giacomo

On Tue, Apr 30, 2024 at 2:49 PM Sefcikova, Jana <j.sefcikova_at_northeastern.edu<mailto:j.sefcikova_at_northeastern.edu>> wrote:
Hi,

Is it possible to restart calculations (either in Minimization or MD simulation step of QwikMD) from the last step? If so, HOW?

I am running QwikMD on a university computer cluster with assigned/limited time and processors allocation. The cluster administrators assigned to my account 24 hours and 28 processors, which is not enough to finish either 500000-steps minimization or 500000-steps MD simulation. After 24 hours, my jobs are terminated including VMD.

Thanks,
Jana

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