title: Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.
abstract: Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field.
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Maryland, 21201.
authors.forename: Justin A
authors.initials: JA
authors.lastname: Lemkul
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637.
authors.forename: Benoît
authors.initials: B
authors.lastname: Roux
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
authors.forename: David
authors.initials: D
authors.lastname: van der Spoel
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Maryland, 21201.
authors.forename: Alexander D
authors.initials: AD
authors.lastname: MacKerell
mesh_terms: D000465:Algorithms; D006801:Humans; D056004:Molecular Dynamics Simulation; D012984:Software; D013816:Thermodynamics; D025801:Ubiquitin / Q000737:chemistry; D014867:Water / Q000737:chemistry
chemical_list: D025801:Ubiquitin; D014867:Water
keywords: induced polarization; molecular dynamics; parallel performance; scalability