title: The fast multipole method and point dipole moment polarizable force fields.
abstract: We present an implementation of the fast multipole method for computing Coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected O(N) scaling of that approach by performing single energy point calculations on hexamer protein subunits of the mature HIV-1 capsid. We also show the long time energy conservation in molecular dynamics at the nanosecond scale by performing simulations of a protein complex embedded in a coarse-grained solvent using a standard integrator and a multiple time step integrator. Our tests show the applicability of fast multipole method combined with state-of-the-art chemical models in molecular dynamical systems.
authors.affiliation: Exascale Research Computing Lab, Campus Teratec, 2 Rue de la Piquetterie, 91680 Bruyeres-le-Chatel, France.
authors.forename: Jonathan P
authors.initials: JP
authors.lastname: Coles
authors.affiliation: Laboratoire de Biologie Structurale et Radiobiologie, Service de Bioénergtique Biologie Structurale et Mécanismes, Institut de biologie et de technologies de Saclay, CEA Saclay, F-91191 Gif sur Yvette Cedex, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Masella
mesh_terms: D036022:Capsid Proteins / Q000737:chemistry*; D005583:Fourier Analysis; D015497:HIV-1; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D036022:Capsid Proteins; D012997:Solvents