Lammps trajectory in VMD with correct atoms connectivity

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1

Dear Everyone,

I have a quick question: for visualizing the trajectory output from Lammps by using VMD.

I did the following: (1) in VMD TKconsole, read the Lammps data file: topo readlammpsdata data.mymolecular

(2) in VMD main window, select File -> Load data into molecule (here I select the dump.xyz file from Lammps)

I want to make sure if this procedure is correct to view Lammps trajectory in VMD with correct atom connectivity (bond, angle, dihedral,...) that I defined in the data file.

Thanks a lot!

Lili

2

Dear Everyone,

I have a quick question: for visualizing the trajectory output from Lammps
by using VMD.

I did the following: (1) in VMD TKconsole, read the Lammps data file: topo
readlammpsdata data.mymolecular
(2) in VMD main window, select File -> Load data into molecule (here I
select the dump.xyz file from Lammps)

I want to make sure if this procedure is correct to view Lammps trajectory
in VMD with correct atom connectivity (bond, angle, dihedral,...) that I
defined in the data file.

the only way to make certain is to inspect the visualization very
carefully. while the procedure you describe is theoretically correct,
it is practically impossible to confirm from remote that you actually
executed it correctly.

if you have doubts, then it is best to construct a small test case and
inspect your procedure very carefully.

axel.

3

Thanks Dr. Kohlmeyer. I read your tutorial https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial—various-tips-tricks
and I seems that you first read in the Lammps data file, then further use topo to retype bonds, angle, dihedral, and improper, and then reanalyze the system. For example:
topo readlammpsdata data.hdpe-x5 full
topo guessatom element mass
topo guessatom name element

topo guessatom radius element
mol reanalyze top

animate write psf hdpe-x5.psf

animate write pdb hdpe-x5.pdb

This is why I doubt my procedure, I feel I missed several steps (as listed above) after read in the lammps data file .

I will test on a small system to verify my procedures.

Many thanks,

Lili

4

Thanks Dr. Kohlmeyer. I read your tutorial
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks
and I seems that you first read in the Lammps data file, then further use
topo to retype bonds, angle, dihedral, and improper, and then reanalyze the
system. For example:
topo readlammpsdata data.hdpe-x5 full
topo guessatom element mass
topo guessatom name element
topo guessatom radius element
mol reanalyze top
animate write psf hdpe-x5.psf
animate write pdb hdpe-x5.pdb
This is why I doubt my procedure, I feel I missed several steps (as listed
above) after read in the lammps data file .

that all depends on what kind of information you want to try and
recover from the data file. a lammps data file contains only the
information that is required to run the simulation, but programs like
VMD sometimes expect certain additional information to make certain
visualizations work as expected. the steps you quote try to recover as
much as possible (which in turn loses the corresponding information
directly from LAMMPS). so you have to make a choice.

axel.