Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

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TitleImplementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.
Publication TypeJournal Article
Year of Publication2015
AuthorsLemkul, JA, Roux, B, van der Spoel, D, Mackerell, AD
JournalJ Comput Chem
Volume36
Issue19
Pagination1473-9
Date Published2015 Jul 15
ISSN1096-987X
KeywordsAlgorithms, Humans, Molecular Dynamics Simulation, Software, Thermodynamics, Ubiquitin, Water
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.

DOI10.1002/jcc.23937
Alternate JournalJ Comput Chem
PubMed ID25962472
PubMed Central IDPMC4481176
Grant ListR01 GM072558 / GM / NIGMS NIH HHS / United States
R01 GM070855 / GM / NIGMS NIH HHS / United States
GM051501 / GM / NIGMS NIH HHS / United States
GM070855 / GM / NIGMS NIH HHS / United States
F32GM109632 / GM / NIGMS NIH HHS / United States
F32 GM109632 / GM / NIGMS NIH HHS / United States
R01 GM051501 / GM / NIGMS NIH HHS / United States
R29 GM051501 / GM / NIGMS NIH HHS / United States
GM072558 / GM / NIGMS NIH HHS / United States