VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Mar 10 2015 - 07:44:19 CDT

On Tue, Mar 10, 2015 at 11:53 AM, Albert Solernou
<a.solernou_at_leeds.ac.uk> wrote:
> Hi John,
> thanks for the answer. Although it is not the ideal solution, and although I
> don't know tcl... I could give it a go. Could you point me to the right
> documentation?

http://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/

> In addition I have a few extra questions:
> - Will I be able to define/label different bodies or parts so that I can
> click on them, change colors, and show/hide?

nope. VMD is not really a good tool for such things. you might be
better off to look into a tool like ParaView or VisIt, for example.

http://www.paraview.org/

https://wci.llnl.gov/simulation/computer-codes/visit

> - In that case how will that integrate with the next timestep given that it
> is a "different" molecule?

each timestep has to be a "molecule" (i.e. in "molecule" in VMD is the
term for dataset), the rest is handled by the plugin GUI, which
emulates the regular animation controls and instead shows/hides
individual molecules/datasets

> - I have currently a Tkinter interface that I plan to port to, and I read
> that you support it. Could you point me to the right documentation site to
> do so? Do you have any suggestion?

Tkinter is a significant challenge with VMD, since python runtimes are
so incredible non-portable and so large that they are no longer
bundled with VMD. so to have access to tkinter, you first will need to
compile a custom version of VMD that includes python.

axel.

>
> Cheers,
> Albert
>
>
> On 03/09/2015 06:00 PM, John Stone wrote:
>>
>> Hi,
>> At present, VMD doesn't provide for time-varying mesh data.
>> In the short term, you could overcome this limitation by loading
>> different trajectory timesteps into separate molecules. Once loaded
>> you can animate the mesh trajectory using the multimolanim plugin.
>> Let us know if you need help to get this working.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Mon, Mar 09, 2015 at 03:11:26PM +0000, Albert Solernou wrote:
>>>
>>> Dear all,
>>> I am writing a new plugin that should enable VMD to work with Finite
>>> Element Trajectories. Currently, my plugin reads correctly the input
>>> file, through:
>>> plugin.open_file_read
>>> then loads and displays the surface triangles through:
>>> plugin.read_rawgraphics
>>> and finally releases my handler:
>>> plugin.close_file_read
>>>
>>> The next step should be to load the whole trajectory, and this is
>>> where I need some advice. I understand that this should be done
>>> through:
>>> plugin.read_next_timestep
>>> but, will it update the vertices of the triangles? How can I do so
>>> using molfile_timestep_t? Is there an easy workaround?
>>>
>>> Thanks in advance,
>>> Albert
>>>
>>> --
>>> ---------------------------------
>>> Dr Albert Solernou
>>> EPSRC Research Fellow,
>>> Department of Physics and Astronomy,
>>> University of Leeds
>
>
> --
> ---------------------------------
> Dr Albert Solernou
> EPSRC Research Fellow,
> Department of Physics and Astronomy,
> University of Leeds
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.