From: Vlastimil Zíma (zima_at_karlov.mff.cuni.cz)
Date: Wed Apr 16 2014 - 05:28:56 CDT
Resolution: Finally I found where the bug was - the system was corrupt.
When I removed extra water from my system I did it on per atom (not per
molecule) basis in several cases, which left H and OH chunks of water
molecules. These molecules hadn't integer charges with lead to non-neutral
system. This was most likely the reason which manifested as margin errors.
Since I fixed this I haven't encountered these errors.
2014-02-26 13:38 GMT+01:00 Vlastimil Zíma <zima_at_karlov.mff.cuni.cz>:
> Hi everyone,
> I lately get stuck with my simulation on margin errors which repeats in my
> I have a system of transmembrane protein in a lipid bilayer in water much
> like the one from NAMD membrane tutorial. I did fairly similar set of
> simulations as in tutorial, but after 0,5 ns equilibration with protein
> constrained and 3 ns of equilibration I still can not make a 1 ns
> simulation without margin error, not even with margin 10, which is in my
> experience pretty high, I usually get along with margin 2-3.
> I though of useConstantArea option, but according to the XST files
> dimensions have not converged. On the other hand, system volume is pretty
> I tried to run the simulation with output every step, but these did not
> produce the margin error.
> All configuration files and the last output are available here:
> Not to be confused, files named *_run are still an equilibration.
> Is it possible that there is a bug in pressure control which prefers
> extension in Z dimension at cost of reduction in X and Y dimensions?
> Thanks for any suggestions
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