Which units should I use in molecular dynamics simulation? I have written a simple molecular dynamics simulation program. The simulation runs fine but the physical properties (in particular, I have calculated temperature) are off by many scales. I understand that this might be due to not using the proper dimensionless units for the parameters and variables. How should I choose the units? Are there different methods for  doing this? I would appreciate if someone could provide a good reference regarding this.
 A: The possible choices of sets of units for your simulations is probably infinite, so the answer is ultimately going to be choose a set of units that fit what you need & run with it.
For instance, suppose you want to study the Argon interacting via the Lennard-Jones potential, an appropriate choice of units could be mass, $\mu$, length, $\sigma$, and energy, $\varepsilon$ (which would then allow you to define all other relevant scales via products & divisors of the three) with the scales defined as
$$
\sigma=3.4\times10^{-10}\,\rm m\\
\mu=6.69\times10^{-26}\,\rm kg\\
\varepsilon=1.65\times10^{-21}\,\rm J
$$
all of which are related to the properties of Argon & the L-J potential. If you are studying some other atom/molecule or a different potential, you'll want to scale the different quantities to the properties of the atom/molecule/potential you are interested in. 
It might also be worthwhile to look into the literature for the scalings used by other people studying the same thing as you.
I had suggested in another answer that you should be defining your initial conditions in physical units, then scaling them appropriately after the IC has been set. For output/visualization purposes, you would want to re-scale the quantities to have physical values for display.
A: LAMMPS is a well known molecular dynamics simulation code, here is their documentation on the pages where they discuss units.
http://lammps.sandia.gov/doc/units.html
