I ran molecular dynamics simulation with a molecule of methylcyclohexane soaked into a water box. On the other hand I ran Monte Carlo with the molecule alone (no soaking). I performed this for the equatorial and axial conformers.
The axial conformer with MD stayed axial (the methyl group). The equatorial with MD stayed equatorial. So far no visual change. Is there a way to compute the average energy in VMD for these systems (I have around 250 frames).
On the other hand, the axial conformer alone with MC was transformed into equatorial. While the equatorial stayed the same (visually speaking).
I am trying to understand what's happening here. What I read is that always the equatorial configuration is more stable as it has less steric hindrance (BTW I am computer scientist learning this), so this explains the interconversion in Monte Carlo simulation from axial to equatorial.
On the other hand, I would expect also that in MD the axial conformer turn into equatorial but it didn't, what I believe here is that the water molecules are having some "Solvation effect" on the methylcyclohexane that prevents the interconversion.
So I would like to know if my thought are good and if you could give some references to get more info about solvation effects.