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:
http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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