AMBER Archive (2003)

Subject: Re: How to control box size

From: David A. Case (case_at_scripps.edu)
Date: Wed Jan 22 2003 - 10:53:02 CST

On Wed, Jan 22, 2003, pu xuemei wrote:

> I solvate one enzyme with acetonitrile in xleap,as follows
>
> solvatebox x ACN 10.0
> Solute vdw bounding box: 56.888 45.091 46.347
> Total bounding box for atom centers: 76.888 65.091 66.347
> Solvent unit box: 6.343 4.237 4.237
> Total vdw box size: 69.769 67.795 67.795 angstroms.
> Volume: 320669.682 A^3
> Total mass 119968.943 amu, Density 0.621 g/cc
> Added 2309 residues.
>
> The question is that I don't understand why x dimension(69.769) in "Total
> vdw box size" is smaller than that (76.888) in "Total bounding box for atom
> centers".

The "total bounding box" is just 2 * 10.0 Ang. greater than the solute vdw
bounding box. Where solvent molecules go depends on where they will fit. It
would probably be better to get an equilibrated acetonitrile box first, and
use that, since you do seem to have a pretty small distance between the solute
and x-dimension of your box. But you should visually examine the output to
see how well things are solvated, and what happens with various values for the
input parameters.

..good luck...dac 

-- 

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