From: Aron Broom (broomsday_at_gmail.com)
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 <dexterwy_at_gmail.com> 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
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:49 CST