VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Dec 15 2021 - 09:28:58 CST

VMD expects that atom identities do not change.

It won't be easy to import existing trajectory files. It may work if you
remove the atom ID columns
Or you could use a different file format that doesn't store atom IDs (e.g.
.xyz, but that has other limitations).
You can also try setting the LAMMPSMAXATOMS environment variable before
launching VMD to the largest atom ID in your file. Then the LAMMPS
trajectory reader will create dummy atoms and put them all to a single
location (0.0 0.0 0.0 by default). see
https://urldefense.com/v3/__https://sites.google.com/site/akohlmey/software/lammps-vmd-plugin__;!!DZ3fjg!s_OI_YhSMlQ_FhJJXi70O_epahCZRNExt8BhDhYUC9ej619xRdemrwh_FVjxDoNJVw$

On Wed, Dec 15, 2021 at 10:11 AM Jiabin You <jiabinyou123_at_gmail.com> wrote:

> Dear VMD users:
>
> I used delete_atoms and create_atoms commands many times in the LAMMPS
> input scripts, the total number of atoms at each timestep is unchanged but
> with a discontinuity ATOMS ID.
> When I loaded the LAMMPS dump trajectory into VMD, there is always a
> warning that ignoring out of range atom #*** with id *** and the atoms
> created by the 'create_atoms commands' are all in the same position (0, 0,
> 0) with a strange structure, which is wrong from my original settings. Is
> there any suggestion to modify this to load the 'complete' trajectory into
> VMD for further analysis? Or a continuous ATOMS ID is strictly requested
> for the loading process?
>
> Thank you in advance.
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!s_OI_YhSMlQ_FhJJXi70O_epahCZRNExt8BhDhYUC9ej619xRdemrwh_FVjIojChUA$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.