VMD-L Mailing List

From: Taco de Wolff (tacodewolff_at_gmail.com)
Date: Mon Mar 28 2011 - 05:02:10 CDT

VMD developers,

I am using VMD for my research project and it really a great visualizer.
There is only one thing that bothers me and that is the following:

If I have an example file as such:
ITEM: TIMESTEP
1
ITEM: NUMBER OF ATOMS
24
ITEM: BOX BOUNDS xy xz yz
0.000000 3.048120 0.000000
0.000000 3.046597 0.001523
0.000000 3.046597 0.000000
ITEM: ATOMS id type mol x y z
1 1 0 1.028125 1.523299 2.970434
2 1 0 0.077651 1.523299 2.970434
3 1 0 0.077174 1.523299 2.019955
4 1 1 2.021440 1.523299 2.970434
5 1 1 2.971911 1.523299 2.970434
6 1 1 2.971434 1.523299 2.019955
7 1 2 2.019995 1.523299 0.076163
8 1 2 2.970469 1.523299 0.076163
9 1 2 2.970945 1.523299 1.026642
10 1 3 1.026679 1.523299 0.076163
11 1 3 0.076209 1.523299 0.076163
12 1 3 0.076685 1.523299 1.026642
13 2 4 1.276092 1.523299 2.246866
14 2 4 0.800855 1.523299 2.246866
15 2 4 0.800617 1.523299 1.771627
16 2 5 1.772750 1.523299 2.246866
17 2 5 2.247985 1.523299 2.246866
18 2 5 2.247747 1.523299 1.771627
19 2 6 1.772027 1.523299 0.799731
20 2 6 2.247264 1.523299 0.799731
21 2 6 2.247503 1.523299 1.274970
22 2 7 1.275370 1.523299 0.799731
23 2 7 0.800134 1.523299 0.799731
24 2 7 0.800373 1.523299 1.274970

I have 24 atoms of 8 chains, with four chains per 'type'. I would like
to select all atoms of one type in VMD, and apply a different kind of
representation (color actually).
This works perfectly fine in the case you only load the lammpstrj
file. However, when coupled with a PSF file (using the PSF plug-in) it
seems type (and mol I think) data are vanished.

Is this a bug, or should type data be defined in the PSF file instead
of the LAMMPS file? How can I select a group of atoms based on their
'type'?
Thank you!

My PSF file looks like so:
PSF

       1 !NTITLE
 REMARKS generated PSF file,usage: vmd -psf filename.psffilename.lammpstrj

      24 !NATOM
       1 1 UNK 1 1 0.000000 12.0000 0
       2 1 UNK 1 1 0.000000 12.0000 0
       3 1 UNK 1 1 0.000000 12.0000 0
       4 2 UNK 1 1 0.000000 12.0000 0
       5 2 UNK 1 1 0.000000 12.0000 0
       6 2 UNK 1 1 0.000000 12.0000 0
       7 3 UNK 1 1 0.000000 12.0000 0
       8 3 UNK 1 1 0.000000 12.0000 0
       9 3 UNK 1 1 0.000000 12.0000 0
      10 4 UNK 1 1 0.000000 12.0000 0
      11 4 UNK 1 1 0.000000 12.0000 0
      12 4 UNK 1 1 0.000000 12.0000 0
      13 5 UNK 1 1 0.000000 12.0000 0
      14 5 UNK 1 1 0.000000 12.0000 0
      15 5 UNK 1 1 0.000000 12.0000 0
      16 6 UNK 1 1 0.000000 12.0000 0
      17 6 UNK 1 1 0.000000 12.0000 0
      18 6 UNK 1 1 0.000000 12.0000 0
      19 7 UNK 1 1 0.000000 12.0000 0
      20 7 UNK 1 1 0.000000 12.0000 0
      21 7 UNK 1 1 0.000000 12.0000 0
      22 8 UNK 1 1 0.000000 12.0000 0
      23 8 UNK 1 1 0.000000 12.0000 0
      24 8 UNK 1 1 0.000000 12.0000 0

      16 !NBOND: bonds
       1 2 2 3 4 5 5 6
       7 8 8 9 10 11 11 12
      13 14 14 15 16 17 17 18
      19 20 20 21 22 23 23 24

       0 !NTHETA: angles

       0 !NPHI: dihedrals

       0 !NIMPHI: impropers

       0 !NDON: donors

       0 !NACC: acceptors

       0 !NBOND: donors

       0 !NNB

       0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0

       1 0 !NGRP
       0 0 0