VMD-L Mailing List

From: Kathleen Barron (kathleen.barron_at_gmail.com)
Date: Thu Jul 26 2007 - 11:04:33 CDT

Hi,
I'm pretty new to molecular dynamics simulations and I've been trying to use
vmd to visualize a simulation of a deposition process that I've run in
lammps. For the deposition I'm inserting a new atom into the simulation
every N timesteps. I'm using the 1.8.6 version of vmd and trying to
visualize directly from the lammps trajectory. VMD loads and visualizes
fine, until it reaches the first timestep where a new atom is added. At
that point it cuts off with an error message: "wrong number of atoms in
timestep."
Am I doing something wrong or is vmd just not able to handle lammps outputs
where the number of atoms does not remain constant through the simulations?
And if I can't visualize straight from the lammps trajectory, what's the
next easiest way?
Thanks,
Kathleen