Re: AMBER: How are water molecules at cutoff being treated?

From: David A. Case <>
Date: Tue, 16 Jan 2007 15:36:07 -0800

On Tue, Jan 16, 2007, Li Su wrote:

> I am wondering how amber is treating water molecules in the direct space
> when using PME in the case that some atoms are within cutoff and some atoms
> are out of cutoff ...

Atom pairs within the cutoff are considered in the direct space sum; those
pairs outside the cutoff are ignored. The idea is that the erfc() switching
function is so small by the time you reach the cutoff that nothing would be
gained by doing the longer-pair distances anyway.

> ....and when calculatiing cutoff whether it is done based on
> atom-atom sense or using the center( if so,mass center or geometric
> center?) of the water.

Amber uses atom-based cutoffs (not molecule-based).


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Received on Wed Jan 17 2007 - 06:08:37 PST
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