VMD-L Mailing List

From: Tamara Rogers (talmesha_r_at_yahoo.com)
Date: Fri Sep 29 2006 - 04:04:33 CDT

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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