Dear LAMMPS Users,

The thing is I’m having trouble understanding how lj unit system and the interconversion of real to lj and lj to real units works. I thought I knew. I went through its documentation several times but I’m still having hard time figuring out very basic stuff on my own. So kindly validate whether I’m going in right direction or not.

Just like in SI system we have 7 fundamental quantities with mass, distance, time etc. and everything else is derived from these. Similarly, In lj unit system, we have m, \sigma and \epsilon and rest other quantities are derived from these three. mass is written in m units, distance in \sigma units and energy in \epsilon units. By default LAMMPS sets the value of m, \sigma and \epsilon (& k_B as well) fundamental quantities to 1. So far so good?

Now, Suppose I have a graphene sheet with 100 atoms. The molar mass of carbon is 12.011 g \space mol^{-1}. So, I’ll simply calculate per atom mass of carbon which is 1.99 e-26 Kg but since we have to make quantities dimensionless for lj unit system so we have to divide it by m (which would also be in kg)? This is where my understanding gets a jolt. Just to be clear, should I take M to 100*1.99 e-26 Kg and set m to 1.99 e-26 Kg which makes my M^* to be 100. Am I correct in making this assertion? (Since the formula is M^* = \frac{M}{m}). Also, what if I have multiple atoms of different masses?

Moving on, at equilibrium distance r = 2^{1/6} \sigma so based on interatomic distances in the graphene I can set my \sigma = \frac{r}{2^{1/6}} accordingly. Through this I can define my 1*\sigma and based on this rest all the distances will defined in the units of \sigma. Right?

The corresponding Energy value at this, r = 2^{1/6} \sigma will be my epsilon?

Lastly, since the time unit depends on m, \sigma and \epsilon. Suppose I want to run my simulation for 200ps. So I’ll convert it into respective lj units by \tau^* = \frac{200*10^{-12}}{\sqrt{\frac{\epsilon}{m\sigma^2}}}.

P.S. I understand @akohlmey made it very clear **here** to not do MD on your own but since I’ve already started this venture. I can’t not learn just because I don’t have anyone to learn from.