From: Lutz Maibaum (
Date: Tue May 15 2007 - 20:46:25 CDT


thank you for your reply. I can probably still do what I want by following
Axel Kohlmeyer's tutorial, and load additional data into the atom's user
field after the trajectory has already been loaded. This leads me to the
question if all atom properties (occupancy, mass, etc.) are stored on a
per-timestep basis within vmd, or if some of them cannot be changed along
a trajectory?

Of course it would be nice if all these field would be accessible from the
molfile plugin. I would be very interested to hear what your ideas for a
new plugin interface are.


On Tuesday 15 May 2007 11:12, John Stone wrote:
> Lutz,
> At present the molfile plugin interface hasn't yet been extended to
> allow individual plugins to load up arbitrary extra data fields, though
> this is something we are very keen to implement as it will solve exactly
> the kind of scenario you are asking about. I'm hoping to work on this
> over the next few months as we make revisions to the plugin interface.
> I would be happy to involve you and any other interested parties in the
> molfile plugin interface revisions.
> John Stone
> On Thu, May 03, 2007 at 06:07:12PM -0700, Lutz Maibaum wrote:
> > 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]
> >
> >html#chap5_sect3