Journal article
Polarizable Molecular Dynamics in a Polarizable Continuum Solvent
Journal of chemical theory and computation, Vol.11(2), pp.623–634-634
01/12/2015
DOI: 10.1021/ct500998q
PMCID: PMC4621208
PMID: 26516318
Abstract
We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-term energy conservation can be achieved. This paper is focused on the methodological developments, the analysis of the algorithm, and the stability of the simulations; a proof-of-concept application is also presented to attest to the possibilities of this newly developed technique.
Details
- Title: Subtitle
- Polarizable Molecular Dynamics in a Polarizable Continuum Solvent
- Creators
- Filippo Lipparini - Laboratoire Jacques-Louis LionsLouis Lagardère - Institut des Sciences du Calcul et des DonnéesChristophe Raynaud - Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de MontpellierBenjamin Stamm - Laboratoire Jacques-Louis LionsEric Cancès - MATHematics for MatERIALSBenedetta Mennucci - University of Pisa - Università di PisaMichael Schnieders - University of Iowa [Iowa City]Pengju Ren - University of Texas at Austin [Austin]Yvon Maday - Laboratoire Jacques-Louis LionsJean-Philip Piquemal - Laboratoire de chimie théorique
- Resource Type
- Journal article
- Publication Details
- Journal of chemical theory and computation, Vol.11(2), pp.623–634-634
- DOI
- 10.1021/ct500998q
- PMID
- 26516318
- PMCID
- PMC4621208
- NLM abbreviation
- J Chem Theory Comput
- ISSN
- 1549-9618
- eISSN
- 1549-9626
- Publisher
- American Chemical Society
- Grant note
- DOI: 10.13039/501100001665, name: Agence Nationale de la Recherche, award: ANR-11-IDEX-0004-02; DOI: 10.13039/501100004794, name: Centre National de la Recherche Scientifique
- Language
- English
- Date published
- 01/12/2015
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Biochemistry and Molecular Biology
- Record Identifier
- 9984024519802771
Metrics
19 Record Views