Question about LAMMPS trajectory file visualization

LAMMPS LAMMPS General Discussion
,
1

Dear lammps users,

Sorry for the basic question,
I am trying to visualize the LAMMPS trajectory file via VMD tool.

When I load the dump file with file type ‘LAMMPS trajectory’, I find strange bond in CH4 molecule. More bonds than necessary are expressed in the methane molecule. (as shown in attached figure.) How can I modify the bond information from LAMMPS trajectory file and show the connection among different atoms using VMD? And Is there any recommendation for the visualization of the molecule bonds to show the creation & depletion of chemical bond?

Any advice is very much appreciated.
Thanks in advance.

Best regards,
jongwun

Processing: Methane_bond.jpg…

2

Please note that the trajectory file does not contain any bond information (and unless you explicitly don’t provide it also no information about elements etc. LAMMPS just uses numbers).

VMD assumes bond, element, and other topology information is provided in a separate file, traditionally in .psf format. You could use the TopoTools plugin to generate such a .psf file from a LAMMPS data file and then load it before reading the LAMMPS dump. Homepage of Axel Kohlmeyer - Various Odds & Ends

3

Thank you for your relpy.
I’ll find more about .psf and visit the link.
Thanks again!