Molecular Dynamics Simulations, NVT & NVE
Is anyone aware of all the details and considerations regarding whether to use NVT or NVE ensembles in a MD simulation? (NVE : adiabetic, NVT: constant volume and temperature).
I'm doing a MD simulation to follow the trajectory of an amino acid side chain after I mutate it from a hydrophilic to a hydrophobic residue. My biochemical intuition tells me that in solution, the residue probably rotates so that the hydrophobic side chain can pack against a nearby hydrophobic pocket (which is an entropic effect). I'm inclined to use NVT, but I can't solidly defend that choice. Thoughts?