Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++)

From: Jerome Henin (
Date: Wed Jun 21 2006 - 17:34:23 CDT

On Wednesday 21 June 2006 16:55, Jan Saam wrote:
> Ouch! This is really bad:
> I just found out that NAMD yields different results depending on the
> number of processors used in the calculation!


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 intended more as a general remark than as an answer to your particular
problem, which, again, may have a specific cause.


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