Re: [AMBER] Visualizing average solvent-oxygen density/occupancy from an MD trajectory

From: Daniel Roe <>
Date: Wed, 2 Jul 2014 07:52:28 -0600


You can visualize the density using the 'grid' or 'volmap' commands in
cpptraj. Either command can write an OpenDx ('.dx' extension) or Xplor
('.grid' or '.xplor' extensions) grid, either of which is readable by VMD.
If you are looking to see solvent density around a solute, you will want to
properly orient your system w.r.t. the solute prior to either of these
commands (using e.g. 'rms' and 'center'). The manual has full details on
the keywords for each of these commands.

Hope this helps,


On Tue, Jul 1, 2014 at 6:34 PM, Abhishek Mukhopadhyay <>

> Hi,
> Is there a straightforward way to use an MD trajectory to visualize average
> water's oxygen and hydrogen density (separately) or preferably 3D visualize
> the average solvent polarization of water around a solute using ptraj + any
> of the visualization softwares.
> sincerely,
> Abhishek
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jul 02 2014 - 07:00:04 PDT
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