Discretization

Usually, after running and MD simulation, the first step for constructing an MSM is to discretize the data into a number of micro-states. In the past we have used two types of discretization, either based on the Ramachandran angles or the contact map of the protein. Further details can be found in the following references:

• What is the time scale for alpha-helix nucleation? J. Am. Chem. Soc. 133 (17), 6809-6816 (2011).

• Engineering Folding Dynamics from Two-State to Downhill: Application to lambda-Repressor J. Phys. Chem. B 117 (43) 13435-13443 (2013).

An important detail is that we take advantage of the Transition Based Assignment method, proposed by Buchete and Hummer in their enlightening paper on Master equation models

• Coarse Master Equations for Peptide Folding Dynamics J. Phys. Chem. B 112 (19) 6057–6069 (2008).

For this preliminary part of the analysis we use a combination of Gromacs programs like g_rama and in-house scripts. Although including this step in the package is in my to-do list, it is currently not part of BestMSM.