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

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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