[gmx-users] Restart energy minimization with step .pdb files

[Michele Pellegrino]

Ok, thank you for the clarification; I thought those files where generated no matter what.
By the way, I am not trying to restart because the simulation crashed: it's just that I am running on a cluster and the job exceded the prescibed time limit. The minimimization itself seems to work fine (at least this is what I can see from ener.edr).

Cheers,
Michele

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: 27 February 2020 13:11
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Restart energy minimization with step .pdb files

On 2/27/20 4:37 AM, Michele Pellegrino wrote:
> Hi,
>
>
> I am trying to restart steepest descent using the .pdb files generated by mdrun. The name of these files has the following pattern:
>
> step#%_n*.pdb
>
> being # and * integers and % a character ('a', 'b' or 'c').
>
> I read the documentation, but I can't understand what those files represent.
>
> Could anyone give me some hint?

step*.pdb files are the coordinates in each spatial domain in an attempt
to help you debug what is going on. I have never been able to employ
them in any useful way. All they really indicate is that your mdrun
process is going to crash due to instability.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.