Re: AMBER: size of solventbox

From: Brent Krueger <>
Date: Wed, 23 Feb 2005 15:54:35 -0500

On Feb 23, 2005, at 12:22 AM, Ross Walker wrote:

> This will definitely cause artifacts in your simulation. But it is
> probably
> quite hard to quantify. Perhaps some can comment further. There may be
> some
> work published that tries to quantify the effects of the size of the
> explicit solvent box but I don't know. Note for PME calculations your
> cutoff
> should be about 8A and this needs to be less than half your smallest
> box
> diameter. Hence the smallest axis of your box needs to be larger than
> 16
> angstroms.

The McCammon group did a little work on the issue of artifacts caused
by box size in PME calculations. J Phys Chem B (2000) 104 p.3668-3675.

Probably there is more recent work as well, but not that I'm aware of.


Brent P. Krueger phone: 616 395 7629
Assistant Professor fax: 616 395 7118
Hope College
Department of Chemistry
Holland, MI 49423

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Feb 23 2005 - 21:53:02 PST
Custom Search