What trajectory formats are supported?

General Discussion
1

Hi list,

I cannot find any information on what trajectory files are accepted by Avogadro.
If I go to Extensions->animation->load file, the filter is just “trajectory
files” which is completely unhelpful.

I’d like to convert my COMPASS dump files to some format that can be animated
with Avogadro. If you can suggest a simple format supported by Avogadro I
could use I would be grateful.

Cheers,
Tuukka Verho

2

I’d like to convert my COMPASS dump files to some format that can be animated
with Avogadro. If you can suggest a simple format supported by Avogadro I
could use I would be grateful.

XYZ files (i.e., multiple frames) will work, as will GROMACS trajectories. Parsing new formats is fairly easy, so if you have an example or three, we can add a new format.

Thanks very much,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

3

On Wednesday, April 11, 2012 09:56:47 PM Geoffrey Hutchison wrote:

I’d like to convert my COMPASS dump files to some format that can be
animated with Avogadro. If you can suggest a simple format supported by
Avogadro I could use I would be grateful.

XYZ files (i.e., multiple frames) will work, as will GROMACS trajectories.
Parsing new formats is fairly easy, so if you have an example or three, we
can add a new format.

Thanks very much,
-Geoff

Hi Geoff,

Thanks for your answer. I just realized that LAMMPS (sorry I was talking about
COMPASS in the last mail, that’s the force field I’m using… damn all these
acronyms) can dump data in XYZ and Gromacs formats so there turns out to be no
problem.

The animation (XYZ format) loaded OK but the play button didn’t seem to work
– the only way to animate was to drag the slider. The play button does work
when I create an animation by doing a conformer search, though. I have
Avogadro 1.0.3. You can test with my input file if you wish:

http://consax.net/pilvi/apps/files_sharing/get.php?token=b20c501c33a1a23bb5b7d76340e1884f5267229a

Another observation I made is that if you animate an XYZ file you first have to
open it and then select the file for a second time in the animation dialog.
This is confusing. IMO the animation extension should detect when the loaded
file is a multi molecule file and use it by default in that case.

Thanks for you help.

  • Tuukka
4

The animation (XYZ format) loaded OK but the play button didn’t seem to work
– the only way to animate was to drag the slider. The play button does
work when I create an animation by doing a conformer search, though. I have
Avogadro 1.0.3. You can test with my input file if you wish:

  • Tuukka

Never mind, this seems to be fixed in master.

  • Tuukka
5

On Apr 13, 2012, at 2:00 PM, Tuukka Verho wrote:

The animation (XYZ format) loaded OK but the play button didn’t seem to work
…Never mind, this seems to be fixed in master.

Yes, we sorely need to make a 1.1.0 release real soon now.

Thanks,
-Geoff