VMD-L Mailing List

From: Lutz Maibaum (lutz.maibaum_at_gmail.com)
Date: Thu May 03 2007 - 20:07:12 CDT

Hello,

I have trajectory files created by LAMMPS that contain some additional
information for each atom at every timestep, and I would like to get this
information into VMD to be able to select certain atoms based on that
extra information. I would like to do this directly in the LAMMPS reader
plugin.

The excellent tutorial [1] suggests to use the "user" property of the atom,
but I don't see how I can access that directly from the reader plugin,
since the only quantities defined in molfile_timestep_t are the simulation
box size and the xyz coordinates. Other possible variables that come to
mind (for example, the occupancy value) seem to be defined for the whole
trajectory, not on a per-timestep basis. Is this correct?

Any help would be much appreciated.

  -- Lutz

[1]
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect3