molecular degrees of freedom


I am studying deposition of methyl radical onto a carbon surface.
Before running the dynamics of interaction, I want to equilibrate both the substrate and the molecule at the right temperature (T=1100 K).
I would like to know if it is possible with LAMMPS to define the translational, vibrational and rotational motions of a molecule (CH3) corresponding to a temperature ?


I assume you mean you have many CH3 molecules
on a surface, since the "temperature" of a single
molecule is not well-defined.

If the bonds in each molecule are flexible, then
simply running a normal MD simulation to equilibrate,
where you thermostat the temperature of the system
should suffice. If you run something like Nose/Hoover
(fix nvt in LAMMPS) with chains, then you should
get good equipartition of energy into all the modes
of energy you list, and they will all end up at
the same temperature.

Does that answer your Q?


Thank for your reply Steve,

Actually the basic process was planned to be a single CH3 molecule, previously equilibrated at a given temperature (1100 K), incoming onto a carbon substrate, also previously equilibrated at the same temperature. Both equilibration being performed separately.
So, do you mean that equilibrating a single CH3 molecule is not appropriate ?
Maybe the best way for equilibration would be to model many CH3 molecules, to equilibrate them and then to take a single molecule out of the collection for the deposition process.
What do you think ?
At least in theory, because in practise I am not sure that it is possible. CH3 would probably bind together to form C2H6.

You can take a single flexible CH3 (4 atoms) and
"equlibrate" it at 1100K with a LAMMPS thermostat.
And it will be essentially what you say below, 1 molecule
drawn from an ensemble of similar molecules. The statistics
on 4 atoms vary greatly. So it might be at 1170K. And there
are even less degrees of freedom for vibtational and rotationsl
motion, so I would expect those to be even less close to 1100K.