VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Feb 26 2008 - 12:08:13 CST

On Tue, 26 Feb 2008, Arienti, Marco UTRC wrote:

MA> Hello.

marco,

MA> I am bit puzzled by what box information VMD reads when parsing two
MA> separate LAMMPS trajectory files (both generated with dump_modify no

what trajectory format are you using? lammps native (text),
custom (text), dcd or xtc?

MA> scale), for atoms A and B. The intent is to have atoms of A partially
MA> overlapping a substrate of atoms B. However, while the first lines of
MA> the LAMMPS files describe two boxes with the same extension, overlapping
MA> does not happen in VMD. In fact, the actual coordinates that I see in
MA> VMD seem to be expressed in a completely different sets of units.
MA> What am I doing wrong? The LAMMPS version dates to Jun 2007 (can't
MA> change that). Also, I cannot change the fact that the two sets of atom
MA> come from two different files. The VMD version is 1.8.6

in case you are using the native text format, it is possible that
the lammps molfile plugin does not parse your outputs correctly.

can you upload pieces of both trajectories to the VMD public
biocore project for further inspection (please don't send them
the mailing list).

thanks,
   axel.

MA> Thank you
MA> Marco Arienti
MA>
MA> 

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
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