From: Dive, Aniruddha Mukund (
Date: Tue Nov 17 2015 - 19:05:10 CST


I am running a simulation in lammps with 8 different types of atoms which are clearly defined in the input data file. The simulations are running perfectly and I am able to generate the trajectory in xyz format.

When I try to open this file in VMD the color of atoms in VMD is different. When I check the representation column in display it shows the name of elements as labeled from H to O i.e. from 1-8 as I have 8 atoms i guess. Also if I try to save the co-ordinates into a pdb file, the output pdb file shows different atom name than those were earlier in the data file.

Is there any way I can overcome this issue and have the correct name for atom type as in the input data file.


Aniruddha M Dive

PhD student

School of Mechanical and Materials Engg.

Washington State University