VMD-L Mailing List

From: Liyu Jin (Leo) (liyu.jin_at_monash.edu)
Date: Sun Dec 02 2012 - 06:26:48 CST

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

Leo

On 02/12/2012, at 3:36 PM, John Stone <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
>
> 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