From: Axel Kohlmeyer (
Date: Thu Jul 26 2007 - 12:53:39 CDT


VMD (currently) cannot handle trajectories with a changing number of atoms.
this is why it stops at the first addition of an atom.


On 7/26/07, Kathleen Barron <> wrote:
> 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

Axel Kohlmeyer
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.