cgmd stability

Date: Wed Feb 18 2009 - 17:13:14 CST

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?
> 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.


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