Automatic state partitioning for multibody systems (APM): an efficient algorithm for constructing Markov state models to elucidate conformational dynamics of multibody systems.

The conformational dynamics of multibody systems plays crucial roles in many important problems. Markov state models (MSMs) are powerful kinetic network models that can predict long-time-scale dynamics using many short molecular dynamics simulations. Although MSMs have been successfully applied to conformational changes of individual proteins, the analysis of multibody systems is still a challenge because of the complexity of the dynamics that occur on a mixture of drastically different time scales. In this work, we have developed a new algorithm, automatic state partitioning for multibody systems (APM), for constructing MSMs to elucidate the conformational dynamics of multibody systems. The APM algorithm effectively addresses different time scales in the multibody systems by directly incorporating dynamics into geometric clustering when identifying the metastable conformational states. We have applied the APM algorithm to a 2D potential that can mimic a protein–ligand binding system and the aggregation o...