[gmx-users] Unexpected Production of .pdb files

Warren Gallin wgallin at ualberta.ca
Fri Aug 14 22:26:40 CEST 2009


	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 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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