[gmx-users] purpose of step pdb files during MD

Justin Lemkul jalemkul at vt.edu
Thu Sep 7 14:27:11 CEST 2017

On 9/6/17 5:55 AM, Vedat Durmaz wrote:
> hi guys,
> from time to time i'm faced with GMX output files during MD called, e.g. in the current case:
> step8164372b_n254.pdb
> step8164372b_n2.pdb
> step8164372c_n254.pdb
> step8164372c_n2.pdb
> what i know is that they are related to kind of exploding systems. however, i'm not really able to interpret their content. if i visualize them in VMD, i see a subset of my system surounded by explicit water molecules where the two *n254* files contain a larger part of my fibrils (polypeptides) than the *n2* files which only show few atoms of one particular amino acid. but if i pick certain atoms of the amino acids, they are often not correctly assigned to residue names and the atom index shown in VMD is different from the index listed in the underlying gro file.
> where can i find detailed information about how to interpret the names and contents of these files? why are exactly these atoms written to the pdb files and what does the file name tell me?

These files contain the atoms in a given domain (e.g. on a certain CPU 
core) and are before (b) and after (c) applying constraints of a given 
step.  I personally have never found them to be useful in determining 
anything, but they are an indicator of physical instability.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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