Re: AMBER: &dipole input and some questions on using polarizable force fields

From: David A. Case <>
Date: Wed, 31 Oct 2007 07:38:34 -0700

On Wed, Oct 31, 2007, Seongeun Yang wrote:

> I saw many articles where the box size is as small as just satisftying that the buffer size is only a half of nonbonding cutoff,
> whether the system of interest is small oligopeptides or polypeptides.
> The fact is that some of those articles are highly cited.

This really has nothing to do with the buffer size per se. I personally think
8 Ang is way too small, but others may differ.

Rather, you are simulating a tiny solute, *plus* having a only a small amount
of water. That leads to a total system size that is very small. If this is
really important to you, you should lower skinnb from its default of 2 to 1.
That should enable your simulation to proceed. (Note that the effective
cutoff is cut + skinnb.)

[The problem is this: you start with a system that is just barely big enough
for the minimum image conventions that Amber uses. Then, as the density
increases, the system gets a little smaller, and violates the minimum image
requirements. If you had a bigger solute, you would not see this problem,
even if you kept to the 8 Ang. buffer.]


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Received on Sun Nov 04 2007 - 06:07:09 PST
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