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

From: Eric Pettersen <>
Date: Thu, 3 Jul 2014 12:37:29 -0700

> 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
Hi Abhishek,
        The MD Movie tool in Chimera can do the first thing you requested -- show separate oxygen/hydrogen volumes. You can get Chimera from:

Chimera's MD Movie tool is used to show trajectories. It's documented here:

The part that talks specifically about occupancy analysis (density) is here:

There's a tutorial for ensemble analysis as well, the last part of which covers occupancy analysis. That's here:

I hope this helps.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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Received on Thu Jul 03 2014 - 13:00:02 PDT
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