From: Axel Kohlmeyer (
Date: Tue May 14 2013 - 02:38:00 CDT

On Mon, May 13, 2013 at 10:20 PM, Dave Schall <> wrote:
> Hello,

hi dave,

> I am trying to visualize results from a simulation where charge is a dynamic
> variable. I am using coordinate and charge data output from a LAMMPS dump
> command. The lammps trj file loads no problem into vmd, and I can color
> atoms by charge, but I don't see the charges varying frame to frame (and
> they are varying, I checked). I checked the "update colors every frame" box

this is due to the design decision in VMD. since its original target
was visualize data from conventional bio force fields, properties that
don't change (atom type, radius, number of atoms, charge and so on)
were only stored once per molecule. only coordinates were stored per
frame resulting in huge savings in memory consumption for long
trajectories. there are some additional fields that can store per
frame per atom data (user, user2, user3, user4, vx, vy, vz), but only
the velocity fields are supported by the molfile plugin interface,
which is used to read in trajectories. in the plugin for LAMMPS
trajectories, i've included a little hack that allows you to remap
fields, i.e. you can divert the charge field to the vx property and
thus access the information inside of VMD.

> as well. I seem to recall you need some sort of tcl script if you want to
> update charge for every frame. I have an old script that works for pdb files
> but I am not sure exactly where to start modifying the script to read a
> lammps trj file. Can anybody point me towards a solution?

that is a very cumbersome approach and i don't recommend that. i'd
suggest you use something like this to load the charge information
into the user field.

global env
set mol [mol new lammps.trj type lammpstrj waitfor all]
# insert "mol addfile command here, if needed"
set nf [molinfo $mol get numframes]
set sel [atomselect $mol all]
for {set i 0} {$i < $nf} {incr i} {
  $sel frame 0
  $sel set user [$sel get vx]
  $sel set vx 0.0
$sel delete
unset sel

if you then set Coloring Method to Trajectory->User->User you should
get the visualization you are looking for.

for more info on the lammps molfile plugin, you can go to this page
and if you'd rather do it "the hard way", you can look up some
examples and explanations in this pdf

please let us know if you have any additional questions.


> Thanks,
> Dave
> --
> J. David Schall, Assistant Professor
> Dept. of Mechanical Engineering, Oakland University
> 130 DHE, Rochester, MI 48309
> 248-370-2870

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.