Re: Periodic cell size

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Dec 08 2004 - 11:43:02 CST

Hello

Is your cell size big enough? It may be that a few of the particles are
outside the boundary box.

A more thoughtful answer though would include a discussion about the
applicability of PME to massively charged systems. However, I don't have
the experience discuss that...

Brian

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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**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
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