Re: Keeping water out of the binding pocket with ColVar

From: Aron Broom (
Date: Fri Jul 20 2012 - 20:19:09 CDT

you could certainly do that, but the problem is, which water molecule? If
you just have a distance restraint, you'd have to do it for each water...
Perhaps there is a different colvar that would be better, I don't know.

On Fri, Jul 20, 2012 at 9:14 PM, Wang Yi <> wrote:

> Hi NAMD experts,
> I'm wondering if there's any way to keep the solvent out of the binding
> pocket of a receptor, to sort of create an empty cavity in a solvent box. I
> was thinking about using the "lower wall" feature, but not quite sure how
> to implement it. Or maybe there's better way to do it? Thanks.
> Best,
> ___________________________
> Yi (Yves) Wang
> Duke University

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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