This directory contains Markov state model macro states derived from the 100-microsecond main protease trajectory as published by DE Shaw. We have constructed tICA-based states based either on positions (_pos_) or distances (_dist_), where the latter appear to have slightly nicer and more markovian properties.

The top.pdb file is a GROMACS-format coordinate with atom names and all hydrogens, corresponding exactly to the coordinate data present in the compressed trajectory files. Each such “trajectory” file contains 10 representative structures from the MSM macrostate in question.

It should be straightforward to extract individual PDB files directly from the XTC files using e.g. the GROMACS “gmx trjconv” command, or we can easily do it for you if you do not have that installed.