VMD-L Mailing List

From: Oliver Lanning (lanning_at_physchem.ox.ac.uk)
Date: Wed Sep 08 2004 - 02:59:11 CDT

Hi,

I have been using vmd to display the atom positions from an MD run, using
the xyz format. With vmd 1.8.1 I could read in a number of frames and
play them. In the file at the top I had the number of atoms in each frame
and the number of frames, then for each frame I had a comment line, then
the list of atoms for that frame with each line consisting of an atom
identity and their xyz coordinates. However, during the run the identity
of some of the atoms changes, I am visualising the first coordination
sphere for an atom and am interested in the change of the species in this
shell. It turns out that vmd, whilst reading in the new xyz data at each
frame does not read in the ion identity, so the color stays as it was in
the first frame. Is there any way to solve this problem? With vmd 1.8.2 I
cannot get the program to read in more than 1 frame.

many thanks,

Oliver Lanning

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Oliver Lanning
The Queen's College Physical and Theoretical Chemistry Lab
High Street South Parks Road
Oxford Oxford
OX1 4AW OX1 3QZ