One of the limitations of molecular dynamics is the sampling problem, which refers to the insufficient sampling of target configurational space, due to a large gap between the timescales reachable by simulation (usually microseconds) and slow target conformational changes, which can be many orders of magnitude longer. One method that could potentially solve this is Markov State models.
Amaro, Rommie E., Jerome Baudry, John Chodera, Özlem Demir, J. Andrew McCammon, Yinglong Miao, and Jeremy C. Smith. “Ensemble Docking in Drug Discovery.” Biophysical Journal 114, no. 10 (2018): 2271–78.
One of the limitations of molecular dynamics is the sampling problem, which refers to the insufficient sampling of target configurational space, due to a large gap between the timescales reachable by simulation (usually microseconds) and slow target conformational changes, which can be many orders of magnitude longer. One method that could potentially solve this is Markov State models.