VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 10 2014 - 15:43:58 CDT

On Wed, Sep 10, 2014 at 10:03 PM, Eric Smoll <ericsmoll_at_gmail.com> wrote:
> Thank you, John. I will give it a shot.
>
> What is the "ABI plugin?" I do not see it listed on this page:
> http://www.ks.uiuc.edu/Research/vmd/plugins/

that wasn't what john was talking about. he mean that the way how
plugins communicate with VMD was extended. previously (e.g. when the
trrplugin was written) it was not possible to read in velocities. now
it is possible, but somebody has to update the trrplugin to read and
provide that information to VMD. for that you need to know some
programming and how data is encoded into the trr file format.

axel.

> - Eric
>
> On Wed, Sep 10, 2014 at 1:45 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>
>> If you know the trr format, it would probably be pretty easy to
>> add velocity reading support into the plugin source code.
>>
>> The VMD plugin ABI version 10 added support for velocities many years ago,
>> so it's just a file-format- and plugin-specific coding task to add
>> velocity reading support.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Wed, Sep 10, 2014 at 01:28:56PM -0600, Eric Smoll wrote:
>> > Hello VMD users,
>> > According to this page:A
>> > [1]http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/trrplugin.html
>> > VMD ignores velocities in a gromacs binary trajectory files (xtc and
>> > trr
>> > files.)
>> > If I have a need for velocity information, what is the best way to
>> > configure GROMACS and/or VMD to import this information.
>> > Best,
>> > Eric
>> >
>> > References
>> >
>> > Visible links
>> > 1. http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/trrplugin.html
>>
>> --
>> NIH Center 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/
>
> 

-- 
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.