What is the difference between Molecular Dynamics and Stochastic Dynamics? Which methods should I use?
Molecular dynamics is a constant energy simulation method while Stochastic Dynamics is a constant temperature simulation method. Since most experiments are done at constant temperature, we recommend using the latter. Also, Stochastic Dynamics simulations has a better chance to cross energy barriers (due to the addition of random forces), i.e., they converge faster. Q8.
