VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Apr 30 2024 - 14:42:21 CDT

Hello Jana, it is a good idea to run things interactively from VMD using
QwikMD while learning. However, you will get the most out of the existing
resources if the MD simulation runs unattended in the form of chained batch
jobs.

That means using the information from the log of your interrupted job to
estimate a number of steps that will fit within your job's walltime. You
can then for each new job set the value of outputName to something unique
to that job:
https://www.ks.uiuc.edu/Research/namd/2.14/ug/node12.html#SECTION00062200000000000000

Then the next job will use binCoordinates, binVelocities and extendedSystem
to load the output file of that previous job, while using a distinct
outputName, and so on.

Giacomo

On Tue, Apr 30, 2024 at 2:49 PM Sefcikova, Jana <
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
>
>
>