Re: [AMBER] water cap simulation

From: case <>
Date: Sat, 28 Apr 2012 10:00:20 -0400

On Fri, Apr 27, 2012, Yi An wrote:
> I'm trying to simulate a protein in a water cap. My problem is during the
> equilibration and simulation stages, water molecules come out of the cap so
> the simulation stops.

It would help to have a better description of the symptoms of the failure.
Can you describe what you mean by "water molecules come out of the cap"? Are
there any messages when the simulation stops?

> Looks like I have to use non-periodic boundary water
> caps and I can't use constant pressure ensembles. Is this the reason why
> waters drift out?

This is confusing: water caps can only be used for non-periodic simulations.
It doesn't make sense to have a water cap in a periodic simulation. Is that
what you are trying to do?


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Received on Sat Apr 28 2012 - 07:30:03 PDT
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