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Implementation of extended L agrangian dynamics in GROMACS for polarizable simulations using the classical D rude oscillator model
Author(s) -
Lemkul Justin A.,
Roux Benoît,
van der Spoel David,
MacKerell Alexander D.
Publication year - 2015
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23937
Subject(s) - molecular dynamics , polarizability , force field (fiction) , scalability , polarization (electrochemistry) , physics , drude model , statistical physics , computer science , computational science , chemistry , quantum mechanics , molecule , database
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.