title: Scalable free energy calculation of proteins via multiscale essential sampling.
abstract: A multiscale simulation method, "multiscale essential sampling (MSES)," is proposed for calculating free energy surface of proteins in a sizable dimensional space with good scalability. In MSES, the configurational sampling of a full-dimensional model is enhanced by coupling with the accelerated dynamics of the essential degrees of freedom. Applying the Hamiltonian exchange method to MSES can remove the biasing potential from the coupling term, deriving the free energy surface of the essential degrees of freedom. The form of the coupling term ensures good scalability in the Hamiltonian exchange. As a test application, the free energy surface of the folding process of a miniprotein, chignolin, was calculated in the continuum solvent model. Results agreed with the free energy surface derived from the multicanonical simulation. Significantly improved scalability with the MSES method was clearly shown in the free energy calculation of chignolin in explicit solvent, which was achieved without increasing the number of replicas in the Hamiltonian exchange.
authors.affiliation: Research Program for Computational Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. moritsuguk@riken.jp
authors.forename: Kei
authors.initials: K
authors.lastname: Moritsugu
authors.forename: Tohru
authors.initials: T
authors.lastname: Terada
authors.forename: Akinori
authors.initials: A
authors.lastname: Kidera
mesh_terms: D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D009842:Oligopeptides; D012997:Solvents; C506175:chignolin