From: Grzegorz Wieczorek (grzegorz.wieczorek_at_weizmann.ac.il)
Date: Sun Dec 02 2012 - 04:24:29 CST

Hi,
Also, take a look at gromacs tool called g_spatial. It produces spatial distribution functions in gaussian cube format, which are beautifully displayed by VMD.
Best,

Grzegorz Wieczorek
Dpt. of Structural Biology
Weizmann Institute of Science

________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of John Stone [johns_at_ks.uiuc.edu]
Sent: Sunday, December 02, 2012 6:36 AM
To: Liyu Jin (Leo)
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: use volmap tool for probability density map

Hi,
  From your description, you should first align your trajectory frames
so the interesting portions of your solute structure are relatively unmoving.
Then, you would select the ion/atom that you want to see the probability
density for, and compute the density or occupancy maps, perhaps weighted by
some other factor, depending on what you're hoping to get out of it.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Dec 02, 2012 at 12:56:30AM +1100, Liyu Jin (Leo) wrote:
> Dear VMD users,
> I was looking for the method to plot probability density map to visualize
> the probability of finding a particular kind of ion/atom around a selected
> molecule average over all the frames. And I found the Volmap Tool of VMD
> may be useful. But after some searching and reading I still cannot figure
> out how to use the Volmap tool to fit my purpose. To be specific:
> 1. On the GUI, "selection" should be the selected/surrounded molecule or
> the surrounding atoms?
> 2. "volmap type" should be the "density" ?
> 3. for "average combining all of the frames", will the tool convert the
> coordinates according to the orientational change in different frames of
> the selected "solute" molecule, so that the final isosurface shows the
> "solvent" ions' probability around the single oriented "solute" molecule i
> 1/4*
> any help will much appreciated !
> Cheers
> Liyu Jin (Leo)

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