From: Axel Kohlmeyer (
Date: Mon Aug 29 2011 - 13:20:02 CDT

On Mon, 2011-08-29 at 10:20 -0700, winardi, erik wrote:
> Dear VMD users,

dear erik,

> I have questions about using the lammps.trj output from VMD.
> 1. I tried to use the lammps.trj format datafile for lammps data
> input, I am guessing that I can't use the output of lammps.trj for
> lammps input file. I understand that VMD can use the topo
> writelammpsdata command to provide the initial structure data to
> lammps. I just curious when do we need to provide this lammps.trj data
> in lammps?

i don't really understand your question, which seems to be
more appropriate for the lammps-users mailing list in the
first place. do you want to use a lammps trajectory dump
as input for the read_data command? this is not possible.

> 2. I went trough the topotools website but I couldn't find how the
> data format for topo writelammpsdata is written. I am trying to make a
> converter for different data format to be converted to lammps data
> format. It would be great if I could get the format of writting the
> initial lammps molecule data.

again, this question would be better asked on the lammps-users mailing
list. the format of the lammps data file is documented in great detail
in the lammps manual. look up the documentation of the read_data

what kind of a conversion are you looking for. for the most part
the topotools plugin aims to provide already the infrastructure
to write correctly formatted lammps data files and VMD provides
(through molfile/babel) access to a large variety of input file
formats. the tricky part in between is to generate/reconstruct
the pieces of information that are needed for a proper topology
(i.e. lammps data) file, that are missing from the many existing
coordinate file formats. this is something that is very system
specific and thus it is impossible to write a simple converted.
the (incomplete) topotools tutorial on my home page gives a few
hints at which steps are missing and how to generate the information
for a couple of rather simple systems.

if you can give me a more specific example of the kind of
problem that you want to address, i'd be happy to make further
suggestions or even provide some script templates, if they
are easy enough to do. i would also encourage you to reuse
existing tools as much as possible instead of writing your
own tool from scratch, unless there are very, very good
reasons to do so.

> Many Thanks,
> Erik

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.