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Advanced potential energy surfaces for molecular simulation

Advanced potential energy surfaces for molecular simulation
Advanced potential energy surfaces for molecular simulation
Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.
1520-6106
9811-9832
Albaugh, Alex
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Boateng, Henry A.
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Bradshaw, Richard
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Demerdash, Omar N.
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Dziedzic, Jacek
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Mao, Yuezhi
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Margul, Daniel T.
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Swails, Jason
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Zeng, Qiao
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Case, David A.
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Eastman, Peter
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Wang, Lee-Ping
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Essex, Jonathan
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Head-Gordon, Martin
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Pande, Vijay S.
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Ponder, Jay W.
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Shao, Yihan
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Skylaris, Chris
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Todorov, Ilian T.
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Tuckerman, Mark E.
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Head-Gordon, Teresa
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Albaugh, Alex
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Boateng, Henry A.
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Bradshaw, Richard
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Demerdash, Omar N.
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Dziedzic, Jacek
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Mao, Yuezhi
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Margul, Daniel T.
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Swails, Jason
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Zeng, Qiao
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Case, David A.
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Eastman, Peter
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Wang, Lee-Ping
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Essex, Jonathan
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Head-Gordon, Martin
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Pande, Vijay S.
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Ponder, Jay W.
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Shao, Yihan
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Skylaris, Chris
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Todorov, Ilian T.
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Tuckerman, Mark E.
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Head-Gordon, Teresa
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Albaugh, Alex, Boateng, Henry A., Bradshaw, Richard, Demerdash, Omar N., Dziedzic, Jacek, Mao, Yuezhi, Margul, Daniel T., Swails, Jason, Zeng, Qiao, Case, David A., Eastman, Peter, Wang, Lee-Ping, Essex, Jonathan, Head-Gordon, Martin, Pande, Vijay S., Ponder, Jay W., Shao, Yihan, Skylaris, Chris, Todorov, Ilian T., Tuckerman, Mark E. and Head-Gordon, Teresa (2016) Advanced potential energy surfaces for molecular simulation. The Journal of Physical Chemistry B, 120 (37), 9811-9832. (doi:10.1021/acs.jpcb.6b06414). (PMID:27513316)

Record type: Article

Abstract

Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.

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JPCB_Feature_revise.pdf - Accepted Manuscript
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Accepted/In Press date: 8 August 2016
e-pub ahead of print date: 11 August 2016
Published date: 22 September 2016
Organisations: Computational Systems Chemistry

Identifiers

Local EPrints ID: 402287
URI: http://eprints.soton.ac.uk/id/eprint/402287
ISSN: 1520-6106
PURE UUID: 590c3074-f0dc-4aae-aed9-05c723c03986
ORCID for Richard Bradshaw: ORCID iD orcid.org/0000-0002-8652-4301
ORCID for Jacek Dziedzic: ORCID iD orcid.org/0000-0003-4786-372X
ORCID for Jonathan Essex: ORCID iD orcid.org/0000-0003-2639-2746
ORCID for Chris Skylaris: ORCID iD orcid.org/0000-0003-0258-3433

Catalogue record

Date deposited: 03 Nov 2016 16:11
Last modified: 07 Oct 2020 04:20

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Contributors

Author: Alex Albaugh
Author: Henry A. Boateng
Author: Richard Bradshaw ORCID iD
Author: Omar N. Demerdash
Author: Jacek Dziedzic ORCID iD
Author: Yuezhi Mao
Author: Daniel T. Margul
Author: Jason Swails
Author: Qiao Zeng
Author: David A. Case
Author: Peter Eastman
Author: Lee-Ping Wang
Author: Jonathan Essex ORCID iD
Author: Martin Head-Gordon
Author: Vijay S. Pande
Author: Jay W. Ponder
Author: Yihan Shao
Author: Chris Skylaris ORCID iD
Author: Ilian T. Todorov
Author: Mark E. Tuckerman
Author: Teresa Head-Gordon

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