VMD-L Mailing List

From: Almeida-Hernández, Yasser, Dr. (yasser.almeida-hernandez_at_uni-due.de)
Date: Thu Aug 20 2020 - 03:16:52 CDT

Thank you.

Best,

Yasser

________________________________
From: Axel Kohlmeyer <akohlmey_at_gmail.com>
Sent: Wednesday, August 19, 2020 5:10:46 PM
To: Almeida-Hernández, Yasser, Dr.
Cc: VMD Mailing List
Subject: Re: vmd-l: New LAMMPS atom style for TopoTools

The TopoTools plugin does not read dump files but data files.
It currently supports atom styles atomic, bond, angle, molecular, charge, full, and sphere.
Adding support for most other atom styles is non-trivial (or else it would be already done). The atom style has to be specified explicitly when loading the file since the file format is not self-describing, so the atom style cannot be reliably inferred from the data in the file.

LAMMPS (atom or custom style, text mode) dump files can be read through the lammpstrj molfile plugin.

Axel.

On Wed, Aug 19, 2020 at 10:55 AM Yasser Almeida-Hernandez <yasser.almeida-hernandez_at_uni-due.de<mailto:yasser.almeida-hernandez_at_uni-due.de>> wrote:
Hi all,

I want to visualize some LAMMPS's dump files, but they are written in a
different atom style (other than 'full'). How can I add a new atom style
to TopoTools 1.8? I tried to include it based on the 'full'
  style but it didn't work.

Thanks in advance,
Yasser 

--
Dr. Yasser Almeida-Hernandez
Postdoctoral Researcher
Computational Biochemistry
T03 R01 D45
Faculty of Biology
University of Duisburg-Essen
Universitätsstr. 2, 45117 Essen
Email: yasser.almeida-hernandez_at_uni-due.de<mailto:yasser.almeida-hernandez_at_uni-due.de>
Phone: +49 201 183 2457
--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.