VMD-L Mailing List

From: Michael Doig (michael.doig_at_ed.ac.uk)
Date: Fri Oct 03 2014 - 05:45:02 CDT

Thanks to both John and Felipe for their helpful suggestions. Depending
on circumstances I will either make the movies separately or continue
loading in multiple trajectories for multiple views.

John,
Up until now, I have had all views shown simulataneously (i.e N = V).
However, it would be useful to be able to turn off and move some of the
views over the course of a movie. I didn't realise you could do this. If
you have some example code detailing how to do this, it would be helpful.

Thanks,
Michael.

On 01/10/14 13:43, John Stone wrote:
> Michael,
> If I follow your description, it sounds like you're making movies
> where you have the multiple views shown simultaneously, emulating having
> multiple viewports, as opposed to showing the views as part of some
> sequence.
>
> At present, VMD cannot "clone" or link a molecule in the way you
> describe without an associated memory use penalty, but adding such a
> feature might be interesting for a future version.
>
> Given the limitations of the `current VMD implementation, you would have to
> load the trajectory N times where N is the number of simultaneously
> shown independent views. If you plan to shown a larger number of total
> views V, with N shown at any one time, I would expect that you would still
> only need to load N trajectory copies to achieve this, and that to get to
> V views you would use script commands to menipulate the view matrices for
> the N simultenous views over the course of the movie.
>
> You can effectively program the view matrices for different molecules
> independently by toggling all of them "fixed" and then setting the
> global view transformation matrix repeatedly, while "unfixing" each
> of the molecules one at a time. While "fixed", the changes to the
> global transformation matrices are not applied to a given molecule's
> transformation matrix. While "unfixed", the changes are applied.
>
> Let me know if this makes sense and if you want further information or
> example code.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Wed, Oct 01, 2014 at 01:25:04PM +0100, Michael Doig wrote:
>> Hello,
>>
>> I quite often make movies containing multiple viewpoints, from the same
>> trajectory file. To do this I load in the same trajectory however many
>> times I need to, loading into a new molecule each time, and then move
>> the different "molecules" (trajectories), create the representations
>> required, and then generate a single movie containing all the different
>> required viewpoints. (i.e. a top down view, a side on view, one showing
>> just one molecule type etc....) One issue with this is the very large
>> amount of memory sometimes required , if I have to load the same large
>> trajectory into memory a number of times (sometimes between 4 - 8 times).
>>
>> I am wondering if there is any better way of doing this, such as loading
>> the trajectory in once, and then creating a new "molecule" by cloning
>> (or linking) to the first molecule. This would allow me to have multiple
>> viewpoints, without having the same trajectory file loaded into memory
>> multiple times.
>>
>> I use LAMMPS trajectory files, if that makes any difference.
>>
>> Hope this is clear.
>>
>> Thanks for your help,
>> Michael.
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336. 

-- 
Dr Michael Doig
School of Chemistry
University of Edinburgh  Tel:    +44 131 650 7748
West Mains Road          E-mail: michael.doig_at_ed.ac.uk
Edinburgh EH9 3FJ
United Kingdom
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.