From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Jul 10 2006 - 20:15:33 CDT
To return to the original topic... as Mark noted, it would be helpful
for us to know a bit more about your system, and in particular, what you
mean by the protein looking terrible.
What kind of MD run were you doing? And how far into the run did you get
before you got errors?
> After the minimization, the protein (in a water box) looks terrible in VMD! And in the log file it
> keeps saying "Warning: Bad global exclusion count, possible error!
> Warning: Increasing cutoff during minimization may avoid this.".
> Is the small cutoff value responsible for such a poor representation or can I do something else to
> change it?
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