AMBER Archive (2008)

Subject: Re: AMBER: How to manually adjust periodic boundary conditions (PBC)

From: David A. Case (
Date: Wed Nov 19 2008 - 17:35:33 CST

On Wed, Nov 19, 2008, Chin, Keith B wrote:
> Suppose rather than a box lattice, I wish to apply PBC for hex lattice,
> where a=4.516, b= 4.516, c = 7.435, alpha = 90, beta = 90, gamma = 120.

Amber cannot do this small a unit cell. Basically, the box size must be at
least twice the cutoff + "skin" (usually 1 to 2 Ang.) Your only real
alternative is to simulate several unit cells as one "supercell". A cell size
of 18 Ang. is about the practical minimum for Amber.

> parameter skinnb+cutoffnb: (nonbond list cut) has value 0.12000E+02
> This is outside the legal range
> Lower limit: 0.00000E+00 Upper limit: 0.58665E+01
> Check ew_legal.h

This is basically saying (in jargon) what I said above. It looks like you are
setting the cutoff to 10, which is too large -- you should probably stick to
the default of 8.

...good luck...dac

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