This repository contains the CCMV aptamer simulation data and its analysis using Markov State Model (MSM) in [https://www.preprints.org/manuscript/202301.0553/v1]. The Markov state modelling was done using package pyemma v.2.5.7.
MD simulation input files can be found in the md folder
Trajectory and topology fils can be found in the data folder
MSM construction, validation, and analysis are done in jupyter notebooks: msm_estimation and msm_analysis.