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

[Michele Pellegrino]

I am sorry, but I don't fully understand your answer: do you mean step_XXX.pdb files are generated when atoms are overlapping?
In any case I still do not get the meaning of the labels; what 'a', 'b' and 'c' stand for?

Thank you for your quick response.

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 Quyen V. Vu <vuqv.phys at gmail.com>
Sent: 27 February 2020 11:22
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Restart energy minimization with step .pdb files

It usually happens when you have two or more atoms overlap.
step_XXX.pdb is the lowest energy state that steepest descend can give you
with your input file.
In my opinion, you should look into the log file of energy minimization
step, find out which atom is exerted the maximum force, visualize your
initial input and check is there any atom overlaps with that atom.
Best,

On Thu, Feb 27, 2020 at 10:37 AM Michele Pellegrino <micpel at kth.se> 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?
>
>
> Cheers,
>
> Michele
>
>
> p.s. I am running GROMACS 2019.5
> --
> 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.
>
--
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.