From: Jan Saam (saam_at_charite.de)
Date: Thu Jun 22 2006 - 06:45:47 CDT
Hi Jerome,
Jerome Henin wrote:
> Jan:
>
> In the present case, there might be a particular data corruption problem, but
> I just wanted to mention that NAMD runs are not necessarily reproducible when
> moved from an architecture to another one, or when run on clusters or similar
> parallel environments.
>
> The errors you mention, 'Periodic cell has become too small for original patch
> grid!' and 'Atoms moving too fast' often occur in the case of poorly
> equilibrated systems, but "bad things" leading to instability have a nonzero
> probability of happening anytime. The larger the timestep, the farther from
> zero the probability. Maybe your simulation that worked was just luck :)
>
This is what came to my mind first, but this is a restart of a well
equilibrated system. Also I tried this many times independently which
decreases the probability to just have good or bad luck.
I'm afraid I have to search the cause somewhere else. I really believe
it's a data corruption problem.
I'll ask Gengbin how to test this.
Best, Jan
> This is intended more as a general remark than as an answer to your particular
> problem, which, again, may have a specific cause.
>
> Jerome
>
>
-- --------------------------- Jan Saam Institute of Biochemistry Charite Berlin Monbijoustr. 2 10117 Berlin Germany +49 30 450-528-446 saam_at_charite.de
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