also you might find it useful to look at the WESTPA tutorials, they are set
up to track conditions at the end of short runs and do resubmissions (and
more) based on criteria.
On Thu, Mar 17, 2022 at 1:03 PM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> Chris,
>
> adding to Hai's post, I'd also suggest to use a chain-job script that
> checks for your criteria and does a resubmit only if all conditions are
> met.
>
> With this, you'd maybe create more single trajectory files, but you
> could set in advance, how much computational time you would waste in the
> worst case; and you'd have all files in defined states, since all
> calculations are ended via Amber, not via kill, qdel, or scancel.
>
> IMHO, a direct mechanism, which allowed to flag a running Amber job a
> premature stop condition and would act similar to nstlim had been
> reached, does not exist.
>
> Best,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
> On 03/17/2022 05:10 PM, Hai Nguyen wrote:
> > Hi
> >
> > You can write your own cron script to calculate rmsd and very 15 minute.
> If
> > the rmsd satisfies your criteria, the script can kill the job (depends on
> > how you submit the job, “kill”, “qdel” and so on.
> >
> > Hai
> >
> > On Wed, Mar 16, 2022 at 3:32 PM Chris Lee <
> chrishankyu.lee.mail.utoronto.ca>
> > wrote:
> >
> >> Hi all,
> >>
> >> I'm wondering if there is a way to 'monitor' and pre-emptively stop or
> >> cancel a MD run if certain criteria are met. Right now I want to look
> at if
> >> the RMSD value goes above a certain threshold, but I would be
> interested to
> >> know if there is a general method to do this with other metrics of
> interest.
> >>
> >>
> >> I need to run a huge number of MDs (on the order of 10,000s) and
> ideally I
> >> would like to run all of them on the order of 10s of nanoseconds; but
> >> obviously this will take a huge amount of computational resources and
> take
> >> forever.
> >> I have good reason to believe most of these starting structures will
> have
> >> their RMSD values shoot up high very early on in the simulation, so I
> want
> >> to filter these out and not waste computational time.
> >>
> >> Thanks,
> >> Chris
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Received on Thu Mar 17 2022 - 10:30:02 PDT
