Multiconfigurational Coarse-Grained Molecular Dynamics

ME Sharp and FX Vazquez and JW Wagner and T Dannenhoffer-Lafage and GA Voth, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 15, 3306-3315 (2019).

DOI: 10.1021/acs.jctc.8b01133

Standard low resolution coarse-grained modeling techniques have difficulty capturing multiple configurations of protein systems. Here, we present a method for creating accurate coarse-grained (CG) models with multiple configurations using a linear combination of functions or "states". Individual CG models are created to capture the individual states, and the approximate coupling between the two states is determined from an all-atom potential of mean force. We show that the resulting multi configuration coarse-graining (MCCG) method accurately captures the transition state as well as the free energy between the two states. We have tested this method on the folding of dodecaalanine, as well as the amphipathic helix of endophilin.

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