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Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
2015 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 19, 1473-1479 p.Article in journal (Refereed) Published
Abstract [en]

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 Nose-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.

Place, publisher, year, edition, pages
2015. Vol. 36, no 19, 1473-1479 p.
Keyword [en]
molecular dynamics, induced polarization, scalability, parallel performance
National Category
Chemical Sciences
URN: urn:nbn:se:uu:diva-258741DOI: 10.1002/jcc.23937ISI: 000356974700006PubMedID: 25962472OAI: oai:DiVA.org:uu-258741DiVA: diva2:842571
Available from: 2015-07-21 Created: 2015-07-20 Last updated: 2015-07-21Bibliographically approved

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