Re: AMBER: pmf with respect to a surface

From: David A. Case <>
Date: Sat, 9 Sep 2006 21:14:30 -0700

On Fri, Sep 08, 2006, Rahaman, Asif wrote:
> I would like to compute the potential of mean force between a polarizable
> water molecule POL3 and a calcite surface that I have created. I find that I
> can constrain distances, angles, dihedrals, etc but not single coordinates.
> In other words, I would like X and Y of the Oxygen in my water molecule to
> be unconstrained while Z ( the direction perpendicular to the surface)
> should have an umbrella potential.

Here is a good pointer to get you started:


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Received on Sun Sep 10 2006 - 06:07:36 PDT
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