[gmx-users] Unexpected Production of .pdb files

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 14 22:40:21 CEST 2009

Warren Gallin wrote:
> Hi,
>     I am running GROMACS 4.0.5 on a peptide composed of 10 serine 
> residues in a water box.
>     During the run, there have been several pairs of files being written 
> into the working directory, for example:
>     step20230b_n5.pdb
>     step20230c_n5.pdb
>     When I look at the files in PyMol they appear to contain a slab of 
> water, one or two ions and a fragment of the peptide.
>     I've gone back and checked and the peptide was intact in the 
> starting system that had been energy minimized and had the waters 
> equilibrated.
>     This is only happening in one run (Ser10) and not with two other 
> decapeptides (Asp10 and Gly10) that have een set up and run identically.
>     The run doesn't seem to be affected, it's not throwing errors as far 
> as I can see and continues running.
>     I have not found any mention of this in the manual.
>     Is this some weird glitch in my computer (writing intermediate data 
> to a file?) or a known behavior of GROMACS under some conditions?
>     Just trying to understand what's happening.

These intermediate files are written when mdrun suspects that a crash might be 
imminent, to allow you to diagnose the problem.  Check your .log file for 
messages related to:



> Warren Gallin
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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