Animation extension

General Discussion
1

Hello,

The Animation command under the Extensions menu allows you to load a Trajectory file - what is this file, how do I generate one, could I write it by hand (at least for a small molecule)?

Thanks,

Steve

Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657
swathen@sienaheights.edu

2

On Thu, 17 Dec 2009 01:45:16 -0000, Steven Wathen
SWATHEN@sienaheights.edu wrote:

The Animation command under the Extensions menu allows you to load a
Trajectory file - what is this file, how do I generate one, could I
write it by hand (at least for a small molecule)?

I think the easiest format is simply a carriage-return separated series of
XYZ specs - the number of atoms, a blank line, then each atom and its
three cartesian coordinates followed by a blank line, repeated for each
position. (So, probably pretty easy to write by hand.)

I think it can also use OpenBabel to read in a trajectory from an output
file where capable - I’m not sure for what formats this can be done, but
the .xtc extension suggested is a GROMACS trajectory file. (I think
there’s also a utility to convert AMBER output files to these, but I’ve
never used either format.)

Hope this helps,
-Ian Kirker

3

I think the easiest format is simply a carriage-return separated series of
XYZ specs - the number of atoms, a blank line, then each atom and its
three cartesian coordinates followed by a blank line, repeated for each
position. (So, probably pretty easy to write by hand.)

Yes. This is also known as “XYZ movie” format by some programs – just a bunch of chemical XYZ files.

I think it can also use OpenBabel to read in a trajectory from an output
file where capable - I’m not sure for what formats this can be done, but
the .xtc extension suggested is a GROMACS trajectory file.

We’re definitely open to more trajectory formats. I think Tim added GROMACS because that’s what he uses. If people can point us towards useful formats, we can implement them – it’s not too difficult.

Cheers,
-Geoff