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.
Warren Gallin
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