VMD-L Mailing List

From: Berit Hinnemann (behi_at_topsoe.dk)
Date: Wed Nov 26 2008 - 07:03:06 CST

Hi Roberto,

I remember to have seen a solution in Axel Kohlmeyer's vmd tutorial, where
he explains how to display a changing number of atoms. It is here

http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part4.html#chap6_sect1

Best regards,
Berit
Berit Hinnemann
Research Scientist | Characterization Department | Research & Development
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"Roberto Gaspari" <Roberto.Gaspari_at_empa.ch>
Sent by: owner-vmd-l_at_ks.uiuc.edu
26-11-2008 12:13

To
<vmd-l_at_ks.uiuc.edu>
cc

Subject
vmd-l: Movie of a xyz trajectory

Good morning to all,
I've produced a trajectory with xyz files of a system with three different
atoms. Each frame of the trajectory can be displayed correctly when loaded
alone and all the three atoms have a different colour. When I cat the
frames in a single trajectory file, and load this file to VMD, the
animation starts correctly, but from the second frame on, the colours
don't match anymore the correct atoms.
An example of my trajectory file would be:
3

Fe x1 y1 z1
Cu x2 y2 z2
Au x3 y3 z3
3

Fe x4 y4 z4
Fe x5 y5 z5
Au x6 y6 z6

.............

PS My trajectory frames have a constant number of overall atoms, but the
number of individual species changes at every step.. maybe this can be a
problem?

Best Regards,
Roberto Gaspari

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