VMD-L Mailing List

From: Olaf Lenz (olenz_at_fias.uni-frankfurt.de)
Date: Mon Oct 15 2007 - 02:43:47 CDT

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Hi!

bbickmore_at_comcast.net wrote:
> I'm a complete VMD newbie (I'm using the Mac version,) so this question is probably pretty basic. I can load xyz trajectory files for a periodic system into VMD, but they do not contain the unit cell dimensions. The manual says I can set these via the command line, so I have been trying to figure out how to do it. The only thing I have tried that doesn't give me an error message in the command window is something like this:
>
> set alpha 90

This will set the Tcl-variable alpha, but it has no influence on VMD.

To set the unit cell parameters for a frame (i.e. one set of
coordinates), you have to use

        molinfo 0 set alpha 90

or

        molinfo 0 set {alpha beta gamma} {90 90 90}

to set all three angles.

A probably even better solution for your problem might be to use the VTF
format instead of the XYZ-format for your output file. It is as easy to
use as the XYZ format, and furthermore you can set the unitcell
parameters for every timestep. Find a description of the format here:

 http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/vtfplugin.html

Olaf
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