VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 23 2005 - 15:38:34 CST

Ara,
  The current LAMMPS reader only reads the LAMMPS trajectory files, and
so it is ignoring the atom type fields. You'd need to load a PDB or
some other file in conjunction with the trajectory anyway, and so you
should already be able to do this. What file format are you using to load
the structure into VMD?

  John

On Tue, Feb 22, 2005 at 09:58:25AM -0700, Kooser, Ara S wrote:
> 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
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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