VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Aug 03 2020 - 09:57:20 CDT

you need to search the web more and read the VMD user's guide.
VMD supports native LAMMPS dump files (atom and custom style if in text mode).
LAMMPS also supports generating multiple types of output formats that
are understood by VMD and it can even be interfaces to the molfile
plugin library of VMD to write out all formats that VMD can write.

there also is the topotools plugin to read (many kinds of) LAMMPS data files.

you need to understand the VMD data model better which is explained in
the users guide.
i suggest you follow the simple tutorials for VMD with CHARMM/NAMD
files (.psf and .pdb) unless you have a better understanding of the
process and then it will be easier to switch to LAMMPS style files.

there are also several limitations that the VMD data model and molfile
plugin interface imposes on topology/trajectory data that may or may
not affect you. again, "google is your friend(tm)".

axel.

On Mon, Aug 3, 2020 at 10:43 AM Keister, Bradley <bkeister_at_ucsd.edu> wrote:
>
> I’m new to VMD, and was told that I could visualize LAMMPS output with VMD. I’m assuming this meant .dcd files. When I try to run VMD on a Mac. It asks me to “load a molecule” when in fact I have an output from a molecular dynamics simulation. I’ve read elsewhere that a .psf file might be needed.
>
> Can someone point me to a simple collection of files from a LAMMPS MD run that will load properly into VMD?
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.