VMD-L Mailing List

From: Grzegorz Wieczorek (grzegorz.wieczorek_at_weizmann.ac.il)
Date: Mon Dec 03 2012 - 03:43:40 CST

Hi,
In the help of previously mentioned g_spatial there is an explanation how to align trajectories for that purpose.
Best,
Grzegorz
________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Liyu Jin (Leo) [liyu.jin_at_monash.edu]
Sent: Monday, December 03, 2012 12:36 AM
To: vmd-l_at_ks.uiuc.edu
Cc: John Stone
Subject: Re: vmd-l: use volmap tool for probability density map

Thanks John,

But as a newcomer, I am confused by "first align your trajectory frames". Is this means I need to convert the coordinates of the rest frames according to the first frame, so that effectively the "solute" is not moving at all ? If so, is any code or program somewhere available to do this?

Thanks so much !
Cheers

Liyu Jin (Leo)

Postgraduate in Materials Engineering
ARC Centre of Excellence for Electromaterials Science
Monash University

Phone: +61 3 9905 4924
Email: liyu.jin_at_monash.edu<mailto:liyu.jin_at_monash.edu>

On 02/12/2012, at 3:36 PM, John Stone <johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>> wrote:

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<mailto: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) 

--
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078