VMD-L Mailing List

From: Kooser, Ara S (askoose_at_sandia.gov)
Date: Tue Feb 22 2005 - 10:58:25 CST

Hello all,

   I was testing out the LAMMPS reader in VMD and I noticed that the
format for reading in the LAMMPS trajectory is
%d %d %f %f %f (atomid, ?, x, y, z).

The atomid is actually a number assigned to each atom by LAMMPS. The "?"
is the atom type (either element of ff type).
An example would be for a water box:

ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
5040
ITEM: BOX BOUNDS
0 29
0 38.2612
0 44.7998
ITEM: ATOMS
6 2 0.0128126 0.285326 0.0269111
7 1 0.254263 0.146748 0.0747134
8 2 0.25307 0.161941 0.055462
9 2 0.221114 0.136753 0.0766662

The first column under ITEM: ATOMS is the number assigned by LAMMPS, the
second column is the atom type (in this case 2=hydrogen and 1=oxygen).

I was wondering if it is possible in VMD (once you have read in a LAMMPS
trj) to select by atom type so you can color atoms differently (make 2
be gray and 1 be blue) or create different representations by atom type.

Thanks,
Ara

"There is something to be learned from a rainstorm. When meeting with a
sudden shower, you try not to get wet and run quickly along the road.
But doing such things as passing under the eaves of houses, you still
get wet. When you are resolved from the beginning, you will not be
perplexed, though you still get the same soaking." - Yamamoto Tsunetomo