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 important points here are: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