From: JeJoon Yeon (
Date: Wed Jul 29 2015 - 09:21:41 CDT

Hello all

I'm trying to do two visualization task, but I'm curious what strategy
should I need to choose to apply "user field" in here.

1) O in surface hydroxyl.
I have two files - xyz trajectory, and connection table of atoms
(bonds.reax from LAMMPS).
I might just use xyz trejectory (based on bond distance criteria) and
'Computed selection' option written in the manual. Or, I could use both of
connection table file + xyz file as an external file reading approach.

Which one is easier and faster for this visualization when I use the user
field option? Can I approach to the framewise bond table data using VMD
tcl? If yes, how?

2) Atoms of different molecular ID
My xyz file have 5th column, which contains the molecular ID of all atoms.
I want to visualize the atoms based on molecular ID, and the name of the
atoms. Like "Si with molecular number 1 = red, Si with molecular number 10
= blue".

Which option should I need to choose to use 'user field' option for
visualization? I'm not sure how can I approach to the 5th column of xyz.
I'm not sure about whether the VMD can recognize additional columns if xyz
or not. Should I need to modify xyz to lammps custom trajectory format to
read additional columns using user field?

I really want to learn how to use 'user field' option, I could do lot
better than before if I master this.