AMBER Archive (2008)

Subject: Re: AMBER: twin cut-off radii

From: David A. Case (
Date: Mon Feb 04 2008 - 10:09:51 CST

On Mon, Feb 04, 2008, Sandeep Kaushik wrote:

> I want to simulate a protein to which i have added two metal ions. The
> system has been solvated using explicit water. The problem that i am facing
> is the in order to include the effect of the ion on residues which are
> about 20 A apart i need the cut-off radius to be around 20 A.

This statement is not the case. *All* electrostatic interactions are computed
in explicit water simulations. The value of "cut" only serves to make a
division between those interactions computed via direct sum, and those
computed via the "reciprocal" sum. So you are just shooting yourself in the
foot to try to run with a 20 Ang. cutoff.


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