Work

Implementation of extended L agrangian dynamics in GROMACS for polarizable simulations using the classical D rude oscillator model

Year: 2015

Type: article

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.

Source: Journal of Computational Chemistry

DOI: 10.1002/jcc.23937

Authors: Justin A. Lemkul, Benoît Roux, David van der Spoel, Alexander D. MacKerell

Institutions: University of Maryland, Baltimore, University of Chicago, Uppsala University

Language: English

Topic: Advanced Chemical Physics Studies

Subfield: Atomic and Molecular Physics, and Optics

Field: Physics and Astronomy

Domain: Physical Sciences

Open Access status: bronze

Funders: NIH Office of the Director, National Institute of General Medical Sciences