Generation of initial velocities counts dummy atoms as normal atoms.
When grompp generates initial velocities, it counts all the atoms for the
evaluation of the total kinetic energy. Dummy atoms should not be counted.
Because of this, simulations containing water models with dummy atoms such as
TIP4P, start with a temperature higher than the expected one. In particular, in
a simulation of water with the van der Eerden model (which has the same number
of dummy atoms and real atoms), the initial temperature is exactly twice the one
the user specified in grompp.mdp .