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

[Quyen V. Vu]

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
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