Re: AMBER: size of solventbox

From: Brent Krueger <kruegerb.hope.edu>
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.


Cheers,
Brent

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


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Received on Wed Feb 23 2005 - 21:53:02 PST
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