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.
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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
>
>
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Received on Thu Aug 08 2024 - 12:00:02 PDT
