WEMD is a rare-event sampling technique which involves generation of continuous trajectories and rate constants for the rare event of interest in a rigorous manner.
Weighted Ensemble MD is a multiple-trajectory approach whose basic goal is to get from a known initial state to a target state, thereby learning pathways and rates for the process. In this approach, a reaction coordinate is defined which divides the progress from the initial (unbound) state to the target (bound) state into several slabs, or bins, along the reaction coordinate. Several trajectories are started from the initial state with each assigned an equal probability or weight. After a short time interval, the current bin of each trajectory is determined. Trajectories entering new bins are split or combined to give a predetermined number of trajectories for each bin and the trajectories are reweighted in a rigorous statistical manner. The whole process is iterated to generate a weighted trajectory ensemble, which provides information on transition probabilities and the evolving configurational distribution. Unlike other enhanced sampling methods such as metadynamics, accelerated MD or replica exchange MD, no bias is introduced into the dynamics in this rigorous path sampling method.
This approach can provide rigorous estimates for timescales that are much longer than the simulation time, thereby allowing the straightforward calculation of rate constants without making additional assumptions. In addition, this method provides information on a diversity of pathways generated as part of the weighted ensemble as well as yield ensembles of atomically detailed structures of transient states which could provide more information on metastable and transition states.
For more information of Weighted Ensemble MD, please refer to an excellent review by Zuckerman and Chong, 2017
For examples of previously performed studies in which Weighted Ensemble Molecular Dynamics (WEMD) was the primary method used, see the following example cases:
Weighted Ensemble Molecular Dynamics (WEMD) was also used in the following examples: