AMBER Archive (2005)

Subject: RE: AMBER: non-periodic condition

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Feb 03 2005 - 12:27:30 CST


> 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
well?

All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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