From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 04 2006 - 00:19:00 CDT

Tamara,
  Yes, the LAMMPS plugin documentation is incorrect, but the current
version of the LAMMPS plugin should be doing that correctly. (The original
LAMMPS documentation we used to write the plugin actually didn't describe
the box bounds field at all, so we "guessed" and as you can see the initial
guess there was incorrect. :) It should be possible to "unwrap" LAMMPS
trajectories as can be done with the other formats as well. Which version
of VMD are you using?

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 29, 2006 at 02:04:33AM -0700, Tamara Rogers wrote:
> Dear all,
> I'm curious about the box information that VMD reads when parsing a LAMMPS trajectory file. According to the documentation it reads:
>
> ITEM: TIMESTEP %d (timestep number) ITEM: NUMBER OF ATOMS %d (number of atoms) ITEM: BOX BOUNDS %f %f (alpha, a) %f %f (beta, b) %f %f (gamma, c) ITEM: ATOMS %d %d %f %f %f (atomid, ?, x, y, z) ...
>
> Shouldn't that read
>
> ITEM: BOX BOUNDS
>
> %f %f (xlo, xhi)
> %f %f (ylo, yhi)
> %f %f (zlo, zhi)
>
> As far as I know, in LAMMPS alpha=beta=gamma=90 and hence that information is not stored.
>
> Also, would it be possible to extend the Lammps plugin to handle atoms moving across the periodic boundary? (Sort of the same way there are two options when reading an AMBER trajectory file)
>
> Your comments would be greatly appreciated.
>
> Regards
>
> Talmesha
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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