Re: [AMBER] water cluster analysis

From: Jason Swails <>
Date: Mon, 23 Sep 2013 07:38:44 -0400

On Sun, Sep 22, 2013 at 9:46 AM, Subrata Paul <>wrote:

> Is it possible to water cluster in amber12. ?
> if possible, How ?

It's not clear what exactly you want. You can use the "grid" or "volmap"
commands in cpptraj to compute water densities on a grid (the former is a
simple histogram, the latter is like the 'volmap' routine in VMD). You can
figure out where water tends to 'cluster' this way, although this is
difficult to do unless the solute is held fairly rigid.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 23 2013 - 05:00:04 PDT
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