Using the Brennerc plugin

You can also do the same physics as brennermd entirely within Fungimol.

Unfortunately, although Fungimol can do the physics, it does not yet have code to adjust the temperature or conveniently make any other changes to the velocities of the atoms. Thus you will still need to do the first step described earlier with brennermd to bring the gun to 300K. Or, if you wish, you can simply download this precomputed result and load it into Fungimol with Control-R like any other data file. If you don't initially see the gun, press "v" to adjust the view.

Next let's check that the plugin was really present. Bring the mouse over any atom of the figure and press "/" to display the type of the atom. You ought to see something like:

The cursor is pointing at object 377 which is a BrennerAtom//C,SpaceFill
with velocity (-0.001610, -0.000316, 0.009694)
at position (-21.161055, 7.747831, -4.230297)
with no links
The important points here are: Then press "s" to start time. As described earlier, you may wish to mark half of the figure invisible so you can see what is happening. This generates the same movie that you can see from brennermd, except it gets the job done in one half to one third the time, and you can change the course of the simulation by editing the scene while the physics happens.
Copyright 2003 Tim Freeman <tim@fungible.com>