AMBER Archive (2006)

Subject: Re: AMBER: pmf with respect to a surface

From: David A. Case (case_at_scripps.edu)
Date: Sat Sep 09 2006 - 23:14:30 CDT

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:

   http://amber.ch.ic.ac.uk/archive/200607/0353.html

...dac

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