title: Polarizable molecular dynamics in a polarizable continuum solvent.
abstract: We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-term energy conservation can be achieved. This paper is focused on the methodological developments, the analysis of the algorithm, and the stability of the simulations; a proof-of-concept application is also presented to attest to the possibilities of this newly developed technique.
authors.affiliation: UniversitéPierre et Marie Curie−Paris 06 (UPMC), UMR 7598, Laboratoire Jacques-Louis Lions, Sorbonne Universités, F-75005, Paris, France
authors.forename: Filippo
authors.initials: F
authors.lastname: Lipparini
authors.forename: Louis
authors.initials: L
authors.lastname: Lagardère
authors.forename: Christophe
authors.initials: C
authors.lastname: Raynaud
authors.forename: Benjamin
authors.initials: B
authors.lastname: Stamm
authors.forename: Eric
authors.initials: E
authors.lastname: Cancès
authors.forename: Benedetta
authors.initials: B
authors.lastname: Mennucci
authors.forename: Michael
authors.initials: M
authors.lastname: Schnieders
authors.forename: Pengyu
authors.initials: P
authors.lastname: Ren
authors.forename: Yvon
authors.initials: Y
authors.lastname: Maday
authors.forename: Jean-Philip
authors.initials: JP
authors.lastname: Piquemal
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D013055:Spectrophotometry, Infrared
chemical_list: D010455:Peptides; D012997:Solvents