From: Roger A Larson (
Date: Fri Aug 30 2013 - 16:13:13 CDT

I have recently begun to use VMD to visualize crystals in a polycrystalline material. Currently, I have completed analysis, but I want to generate a different color scheme for each large crystal (grey for the grain boundaries). I import data to VMD from a lammpstrj file, and I would like to know if there is a command I can use to assign each atom to a specific group or if there is a way to import color from this input file.

I guess what I want to ask is, is there a way to import colors from a lammpstrj file? I can write the file, just don't know if there is a command for color customization from importing (I know some exist in the GUI):
ITEM: ATOMS id type xs ys zs color?
0 Cu -5 0 5 green
1 Zr -5 0 5 red
Or perhaps assign a group id?