Re: Periodic cell size

From: Edward Patrick Obrien (
Date: Wed Dec 08 2004 - 10:54:37 CST

Hi Suxing,
  I can't answer your question about limits on periodic cell size, but one
thing I can suggest, if you haven't done so already, is follow the
standard practice of minimizing your system, heating it to the desired
temperature, and equilibrating/production run.

Try minimization first, and see if you get any errors there,

On Wed, 8 Dec 2004, Suxing Hu wrote:

> Hi all:
> I am using the NAMD to simulate ultracold plasmas, which basically consist of
> all charged particles. Such a system is quite extended, normally have a spatial
> size of 50umx50umx100um. I am testing for ~500 particles starting almost from
> zero velocity, but it shows at the first time step the particle velocities being
> huge (>10^15), and even nan (not a number).
> Are there any limits on the size of periodic cell in NAMD? PME is turned on in
> my simulation tests.
> Thanks,
> Suxing Hu

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