Re: cgmd stability

From: Peter Freddolino (
Date: Wed Feb 18 2009 - 20:05:57 CST

Hi Bin,
can I verify that you're using 1-2 exclusions and not 1-4? RBCG is
designed to go with 1-2 exclusions, and any other setting can certainly
cause the problems that you're seeing. If that is not the problem, I'd
recommend looking at your system immediately before you get crashes and
seeing if things are becoming visibly deformed. Have you tried running
without the applied pulling, or with a slower pulling velocity?


BIN ZHANG wrote:
> Dear all:
> I've been experiencing with rbcg using NAMD for a while, and often got
> the error "FATAL ERROR: Bad global exclusion count!" during the
> simulation, even with a time step as small as 5 fs. (This could also
> partially blame the calculation I was doing probably, pulling peptide
> through membrane)
> Searching about the list, I found the following reply from peter:
> > Hi Jiaqi,
> > it is important to understand the source of the bad global exclusion
> > count error: Two atoms which should have an exclusion are not on
> > neighboring patches. This happens a lot in coarse grained systems
> > because they have such long bonds. What do you have exclude set to? And
> > how far apart are your particles?
> > Peter
> If this is the case, I wonder would decrease the number of cpus used,
> or increase the "margin" parameter help in solving the problem? Is
> there other way to systemically reduce the error occurring?
> BTW, I do NOT think this error occurs due to bad initial
> configuration, because it could happen after several ten ns running.
> Thanks a lot.
> Bin

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:22 CST