VMD-L Mailing List

From: Frederick R. Phelan Jr. (frederick.phelan_at_nist.gov)
Date: Mon Mar 14 2005 - 17:26:48 CST

John,

Thanks a million! I was able to read in the data using the xyz format.

One question in regard to that format. On the xyz page, it says the format should be as follows:

atom1 x y z [optional data] atom name followed by xyz coords
atom2 x y z [ ... ] and and (optionally) other data.
etc.

Here, do the names atom1 atom2, etc., corresponds to the different types of atoms in the system, or are they unique tags?

I took it to mean the former, but my result did not come out as I expected, i.e., in my LAAMPS file, I have three different of atoms, so I wrote the file as:

1       0.000   0.000   0.000
1       1.100   0.000   0.000
... {rest of type 1}
2       5.500   0.000   0.000
2       6.000   0.000   0.000
... {rest of type 2}
3      11.000   0.000   0.000
3      12.100   0.000   0.000
... {rest of type 3}

But in the VMD rendering, I only get two different colors for the atoms, green and white.

According to what I have put in, should I not get three colors?

Or do I need a more complex format such as PDB for that?

Thanks again,
Fred Phelan





At 03:14 PM 3/14/2005 -0600, you wrote:

Fred,
  Yes, you've got it right.  If PDB isn't convenient, you could use
one of the simpler file formats like XYZ:
  http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html

The PDB format spec is linked here:
  http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html

  John

On Mon, Mar 14, 2005 at 03:28:10PM -0500, Frederick R. Phelan Jr. wrote:
>  John,
>  Thanks for that response.
>  I think I understand. I would use the option "New Molecule ..." to
>  read in a PDB file to view the atoms in their initial configuration,
>  and then, use the "Load Data into Molecule ..." option to read in the
>  LAMMPS output in order to animate?
>  Is there a standard source (e.g., web page) which describes the PDB
>  format?
>  Thanks again,
>  Fred Phelan


--
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@ks.uiuc.edu                 Phone: 217-244-3349             
  WWW: http://www.ks.uiuc.edu/~johns/     Fax: 217-244-6078
<Date>

Frederick R. Phelan Jr., Ph.D.
Processing Characterization Group
Polymers Division
National Institute of Standards and Technology
NIST, Bldg. 224/Rm. A209
100 Bureau Dr., STOP 8542
Gaithersburg, MD 20899-8543
301.975.6761 (VOX)
301.975.4924 (FAX)
Frederick.Phelan@nist.gov
http://polymers.msel.nist.gov/staff/detail.cfm?SID=146