VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 15 2007 - 13:12:34 CDT

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
  vmd_at_ks.uiuc.edu

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

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078