AMBER Archive (2004)

Subject: Re: AMBER: Amber: what different?

From: David A. Case (
Date: Sun Oct 24 2004 - 09:17:47 CDT

On Thu, Oct 21, 2004, Helios Chen wrote:

> I wonder what difference between "solventbox unit TIP3PBOX 10 1" +
> "solventbox unit TIP3PBOX 10 1"(i.e., do again) and the just one command
> "solventbox unit TIP3PBOX 20 1"? Why the added water molecules and density
> are different? Best Regards.

LEaP puts a small "gap" between boxes so that there are no bad atom-atom
contacts in the initial structure. Also, the way in which it removes atoms
of the "solute" that overlap with the water bath would be different for
repeated small solvations, and one big one. Either or both of these effects
could cause your two cases to give different results (although I don't think
they should be greatly different....)


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