RE: AMBER: non-periodic condition

From: Ross Walker <>
Date: Thu, 3 Feb 2005 10:27:30 -0800

> I am trying to run a MD (a solute and 200 ammonia molecules) without
> periodic condition and the Epot fluctuate a lot, between 1500 and
> -1500Kcal/mol !!!
> Does someone know this problem?
> If I put periodic condition the MD is good...

What size is you cut off? You need to use a much larger cutoff in
non-periodic simulations than you do in periodic PME runs. If you can run a
periodic simulation of your system why do you need to run a gas phase one as

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Thu Feb 03 2005 - 18:53:00 PST
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