MSM/RD

MSM/RD is a general framework to couple Markov state models (MSM) of molecular kinetics with particle-based reaction-diffusion (RD) simulations. The software can also be used to simulate Brownian dynamics of rigid bodies with all the translational and rotational degrees of freedom, potential interactions and Markovian switching. 

The code is written in c++ with python bindings. The software is still in constant development, and there is no official release. Active development of the code is done in this github repository: github.com/maojrs/msmrd 

All the figures in the paper ``Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics'' by Mauricio J. del Razo, Manuel Dibak, Christof Schütte and Frank Noé were generated with this code. The exact data used for the paper is available upon request to the authors.