[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:
> 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:
> 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
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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