Extracting kinetics from replica exchange molecular dynamics and related methods that produce discontinuous trajectories.

Kinetics from Replica Exchange Molecular Dynamics Simulations, L.S. Stelzl and G. Hummer 2017, J. Chem. Theory Comput. http://dx.doi.org/10.1021/acs.jctc.7b00372

The repository provides two examples for extracting kinetics from replica exchange molecular dynamics (REMD):

(1) Extracting kinetics from REMD simulations of alanine dipeptide (Ala2) and comparison to MD. Importantly the ala2-lag-time folder contains everything needed to validate the generated model. This is especially important in the typical use case, when no long equilibrium MD simulations are available.

(2) Extracting kinetics from REMD simulations of a coarse-grained polymer model of the neomycin riboswitch. The extracted kinetics is compared to long MD simulations.