VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon May 03 2010 - 16:47:05 CDT

On Mon, May 3, 2010 at 3:46 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> Hi,
>  VMD is currently designed such that it is assumed that atom counts
> and atomic element do not change over the course of simulation.  This
> allows VMD to significantly optimize various graphics and analysis
> operations by taking advantage of this.  If you want to load simulations
> like you describe into VMD, you will need to load each of the frames as
> a separate molecule, and then use the "multimolanim" plugin to animate
> them etc.

actually, there is now a second option. if one uses the latest alpha/beta
version of VMD or installs the corresponding version of the topotools
plugin from here:
http://sites.google.com/site/akohlmey/software/topotools

there there is a new command:
topo readvarxyz filename.xyz

this generate a dummy molecule that is able to represent all
as many particles of each atom type as are in the whole trajectory.
it will then read and pad the trajectory with dummy atoms. via
a selection "user >0" one should then be able to see only
those atoms that are in each original frame. the drawback of
this version is that bonds are not preserved (to massively reduce
memory consumption) and you have to use dynamic bonds.
... or use multimolanim ;)

cheers,
     axel.

> Cheers,
>  John Stone
>  vmd_at_ks.uiuc.edu
>
>
> On Mon, May 03, 2010 at 10:10:58AM -0400, Maxim Paliy. wrote:
>> Dear VMD experts.
>>
>> What is the best way to produce an animation, where
>> the number of atoms and their names  change between the frames?
>>
>> I try to read the frames from a multi-frame pdb or xyz files that I
>> make  in my simulation.
>>
>> However, it seems, VMD  gets the idea about the number and the names of
>> atoms present
>> from the FIRST frame only.
>>
>> is the there a way to change this?
>>
>> Thanks a lot in advance for any suggestions,
>> Maxim
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
>  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.