From: Vlastimil Zíma (zima_at_karlov.mff.cuni.cz)
Date: Wed Feb 26 2014 - 06:38:23 CST
Hi everyone,
I lately get stuck with my simulation on margin errors which repeats in my
simulation.
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
stable.
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:
https://gist.github.com/vzima/9228435
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
Vlastimil
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