I think people will need more information to help you.
you mention that each steps runs fine individually, but do not run " using
through the code to run the jobs for all windows".
I do not understand that statement, so others here also may not.
maybe you can provide the scripts that "run the jobs for all windows".
this might be related to your job setup and not Amber.
On Thu, Aug 8, 2024 at 2:54 PM Kankana Bhattacharjee via AMBER <
amber.ambermd.org> wrote:
> Dear AMBER users,
>
> Kindly help me to resolve the issue.
>
> Thanks & Regards
> Kankana Bhattacharjee
>
> ---------- Forwarded message ---------
> From: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in>
> Date: Wed, Jul 31, 2024 at 2:00 PM
> Subject: Re: Regarding Advanced Thermodynamic Integration:
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> But, if I run individual say 0th state and run each step individually
> (eqpre1P0, eqpre2P0, eqP0 using pmemd.MPI) then the output file is
> correctly written and finished normally. But when I am using through the
> code to run the jobs for all windows then it is not able to run the
> results. Kindly help me with this (using pmemd.cuda).
>
> Your suggestions would be highly appreciated.
>
> sender notified by
> Mail Track for Gmail
> <https://www.mailtrack.email/?utm_source=watermark&utm_medium=email>
> <https://www.mailtrack.email/?utm_source=watermark&utm_medium=email>
> [image:
> ft34ddz98tt-de616d66631e4648]
>
> On Wed, Jul 31, 2024 at 1:51 AM Kankana Bhattacharjee <
> kankana.bhattacharjee_phd21.ashoka.edu.in> wrote:
>
> > Dear AMBER users,
> >
> > I want to mention that, when performing Advanced TI (Thermodynamic
> > Integration) calculation for my protein-ligand system, I am encountering
> an
> > issue where no rst7 file is generated for the eqNTP4 step. The previous
> > steps (init, min1, min2, eqpre1P0, eqpre2P0, and eqP0) ran successfully.
> > The mdout file for eqNTP4 indicates that the simulation did not run, but
> > no error message is provided. Additionally, I had to apply a noshake mask
> > for the TI region/atoms due to significant deviations in bond length. I
> am
> > using similar settings for all mdin files as those used for the CDK2
> > system in the tutorial.
> > I am attaching my eqNTP4.mdin, eqNTP4.mdout (for the two end states).
> >
> > Your suggestions would be highly appreciated.
> >
> > Thanks & Regards
> > Kankana Bhattacharjee
> > Ph.D. Scholar
> > Department of Chemistry
> > Ashoka University
> > Sonipat, Haryana
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 08 2024 - 12:30:02 PDT
