AMBER Archive (2008)

Subject: AMBER: twin cut-off radii

From: Sandeep Kaushik (
Date: Mon Feb 04 2008 - 03:17:57 CST

Hi all,
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. But then the
waterbox size needs to be increased from 7A to 12A on each side of the
protein. The system now, with cut-off 20 A, takes about 6 days compared to
<2 days when the cut-off used was 8A.
My question is whether there exits a way to provide two cut-offs, one for
protein-protein/ion interactions and the other for water-water interactions.

So that i can reduce the time required by the simulation.

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