In this section, we will consider the technique of transition path sampling Monte Carlo simulation for calculating rate constants [17,18]. This technique is one of many designed to overcome time-scale limitations in gathering statistics on processes driven by rare events, or thermally-activated transitions. When performed correctly, transition path sampling provides a means to gain a statistically significant understanding of reaction mechanisms. One of the most significant example uses of this technique is a recent prediction of rate constants for folding-like transitions in simulations of atomically specific protein fragments in explicit solvent [19].
The code used in this section was downloaded from Berend Smit's Molecular Simulation course webpage.