From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Nov 20 2007 - 09:19:33 CST
Hi Long,
you can get a feel for what causes these errors at
http://www.ks.uiuc.edu/Research/namd/wiki/?NamdTroubleshooting.
The two most important things to do if you're encountering this error
are make sure your system was sufficiently minimized, and look at your
trajectory in vmd (possibly writing to the dcd file at every timestep)
so see if you can see where the instability is occurring.
Best,
Peter
Yinglong Miao wrote:
> Hi, NAMD developers and users,
>
> In some of my simulations, I keep getting error messages like "FATAL
> ERROR: Bad global exclusion count!" and "atoms moving too fast". I am
> wondering whether there are flag values returned when executing
> "minimize" and "run". Let's say, when these commands are executed
> correctly, a flag value of 0 is returned; when above error messages
> come up, a flag value of -1 is returned so that I can do something to
> "guide" the simulation according to the flag value instead of just
> going crashed.
>
> If no such flag values returned in NAMD, could anybody tell me how is
> the error "FATAL ERROR: Bad global exclusion count!" determined? I
> know it could be due to stretched bonds, too close atoms or other
> unphysical structure, but how does it work in computation? And how to
> analyze and evolve the atomic structure to avoid above errors?
>
> Any ideas and suggestions will be greatly appreciated!
>
> Thanks,
> Long
>
> --
> Yinglong Miao
> Ph.D. Candidate
> Center for Cell and Virus Theory
> Chemistry Department, Indiana University
> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> 1-812-856-0981(office); http://ylmiao.dict.cn/mypage/
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