Re: Fatal error when running ABF simulation

From: Giacomo Fiorin (
Date: Tue Jun 08 2010 - 08:45:10 CDT

Hello Crick, the problem is not related to ABF but is a recurring issue when
you try to simulate a system that begins outside of equilibrium.

Please check the xst file to see how the box sizes are doing... You will
also find more information on this by searching through the list archives.


---- ----
 Dr. Giacomo Fiorin
 ICMS - Institute for Computational Molecular Science - Temple University
 1900 N 12 th Street, Philadelphia, PA 19122
---- ----

2010/6/8 crazylyf <>

> Hi, everybody,
> I'm now running a ABF simulation of a transmembrane protein, the program
> will aborted after a few steps, and reported message:
> "Fatal error on PE 18> FATAL ERROR: Periodic cell has become too small for
> original patch grid!
> Possible solutions are to restart from a recent checkpoint, increase
> margin, or disable useFlexibleCell for liquid simulation."
> I restarted the system several times and increased the margin to 2.5, also,
> I tried to turn off the useConstantArea, but the problem remains. Should I
> disable useFlexibleCell as the message says? Would this affect the accuracy
> of my simulation?
> Best regards,
> Crick
> ------------------------------
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