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R. Scalco; A. Caflisch

Journal: J. Phys. Chem. B
Year: 2011
Volume: 115
Issue: 19
Pages: 6358-6365
DOI: 10.1021/jp2014918
Type of Publication: Journal Article

Algorithms; Markov Chains; Molecular Dynamics Simulation; Protein Conformation; Protein Folding; Proteins; Thermodynamics


Multiple independent molecular dynamics (MD) simulations are often carried out starting from a single protein structure or a set of conformations that do not correspond to a thermodynamic ensemble. Therefore, a significant statistical bias is usually present in the Markov state model generated by simply combining the whole MD sampling into a network whose nodes and links are clusters of snapshots and transitions between them, respectively. Here, we introduce a depth-first search algorithm to extract from the whole conformation space network the largest ergodic component, i.e., the subset of nodes of the network whose transition matrix corresponds to an ergodic Markov chain. For multiple short MD simulations of a globular protein (as in distributed computing), the steady state, i.e., stationary distribution determined using the largest ergodic component, yields more accurate free energy profiles and mean first passage times than the original network or the ergodic network obtained by imposing detailed balance by means of symmetrization of the transition counts.