VMD-L Mailing List

From: Maxim Paliy. (mpaliy_at_wlu.ca)
Date: Mon May 03 2010 - 19:05:44 CDT

Dear John and Axel,
Thank you very much for you advices,
Ill try both options.
Sincerely yours, Maxim

On 5/3/2010 5:47 PM, Axel Kohlmeyer wrote:
> 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
>>
>>
>
>
> 

-- 
Maxim Paliy              mpaliy_at_wlu.ca
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