AMBER Archive (2006)

Subject: AMBER: pmf with respect to a surface

From: Rahaman, Asif (asif-rahaman_at_uiowa.edu)
Date: Fri Sep 08 2006 - 17:35:22 CDT

Dear Amber users and developers,
 
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.
 
How can I do this?
 
Thanks!
 
Asif
 
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