A graphics processing unit implementation of Coulomb interaction in molecular dynamics

Prateek K. Jha; Rastko Sknepnek; Guillermo Ivan Guerrero-Garcia; Monica Olvera de la Cruz

doi:10.1021/ct100365c

A graphics processing unit implementation of Coulomb interaction in molecular dynamics

Prateek K. Jha, Rastko Sknepnek, Guillermo Ivan Guerrero-Garcia, Monica Olvera de la Cruz

Research output: Contribution to journal › Article › peer-review

42 Citations (Scopus)

Abstract

We report a GPU implementation in HOOMD Blue of long-range electrostatic interactions based on the orientation-averaged Ewald sum scheme, introduced by Yakub and Ronchi (J. Chem. Phys. 2003, 119, 11556). The performance of the method is compared to an optimized CPU version of the traditional Ewald sum available in LAMMPS, in the molecular dynamics of electrolytes. Our GPU implementation is significantly faster than the CPU implementation of the Ewald method for small to a sizable number of particles (similar to 10⁵). Thermodynamic and structural properties of monovalent and divalent hydrated salts in the bulk are calculated for a wide range of ionic concentrations. An excellent agreement between the two methods was found at the level of electrostatic energy, heat capacity, radial distribution functions, and integrated charge of the electrolytes.

Original language	English
Pages (from-to)	3058-3065
Number of pages	8
Journal	Journal of Chemical Theory and Computation
Volume	6
Issue number	10
DOIs	https://doi.org/10.1021/ct100365c
Publication status	Published - Oct 2010

Keywords

FORCES
MONTE-CARLO
ELECTROSTATICS
COMPUTER-SIMULATION
COMPUTATION
FLUIDS
IONIC SYSTEMS
MODEL ELECTROLYTES
BOUNDARY-CONDITIONS

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10.1021/ct100365c

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title = "A graphics processing unit implementation of Coulomb interaction in molecular dynamics",

abstract = "We report a GPU implementation in HOOMD Blue of long-range electrostatic interactions based on the orientation-averaged Ewald sum scheme, introduced by Yakub and Ronchi (J. Chem. Phys. 2003, 119, 11556). The performance of the method is compared to an optimized CPU version of the traditional Ewald sum available in LAMMPS, in the molecular dynamics of electrolytes. Our GPU implementation is significantly faster than the CPU implementation of the Ewald method for small to a sizable number of particles (similar to 105). Thermodynamic and structural properties of monovalent and divalent hydrated salts in the bulk are calculated for a wide range of ionic concentrations. An excellent agreement between the two methods was found at the level of electrostatic energy, heat capacity, radial distribution functions, and integrated charge of the electrolytes.",

keywords = "FORCES, MONTE-CARLO, ELECTROSTATICS, COMPUTER-SIMULATION, COMPUTATION, FLUIDS, IONIC SYSTEMS, MODEL ELECTROLYTES, BOUNDARY-CONDITIONS",

author = "Jha, {Prateek K.} and Rastko Sknepnek and Guerrero-Garcia, {Guillermo Ivan} and {de la Cruz}, {Monica Olvera}",

year = "2010",

month = oct,

doi = "10.1021/ct100365c",

language = "English",

volume = "6",

pages = "3058--3065",

journal = "Journal of Chemical Theory and Computation",

issn = "1549-9618",

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T1 - A graphics processing unit implementation of Coulomb interaction in molecular dynamics

AU - Jha, Prateek K.

AU - Sknepnek, Rastko

AU - Guerrero-Garcia, Guillermo Ivan

AU - de la Cruz, Monica Olvera

PY - 2010/10

Y1 - 2010/10

N2 - We report a GPU implementation in HOOMD Blue of long-range electrostatic interactions based on the orientation-averaged Ewald sum scheme, introduced by Yakub and Ronchi (J. Chem. Phys. 2003, 119, 11556). The performance of the method is compared to an optimized CPU version of the traditional Ewald sum available in LAMMPS, in the molecular dynamics of electrolytes. Our GPU implementation is significantly faster than the CPU implementation of the Ewald method for small to a sizable number of particles (similar to 105). Thermodynamic and structural properties of monovalent and divalent hydrated salts in the bulk are calculated for a wide range of ionic concentrations. An excellent agreement between the two methods was found at the level of electrostatic energy, heat capacity, radial distribution functions, and integrated charge of the electrolytes.

AB - We report a GPU implementation in HOOMD Blue of long-range electrostatic interactions based on the orientation-averaged Ewald sum scheme, introduced by Yakub and Ronchi (J. Chem. Phys. 2003, 119, 11556). The performance of the method is compared to an optimized CPU version of the traditional Ewald sum available in LAMMPS, in the molecular dynamics of electrolytes. Our GPU implementation is significantly faster than the CPU implementation of the Ewald method for small to a sizable number of particles (similar to 105). Thermodynamic and structural properties of monovalent and divalent hydrated salts in the bulk are calculated for a wide range of ionic concentrations. An excellent agreement between the two methods was found at the level of electrostatic energy, heat capacity, radial distribution functions, and integrated charge of the electrolytes.

KW - FORCES

KW - MONTE-CARLO

KW - ELECTROSTATICS

KW - COMPUTER-SIMULATION

KW - COMPUTATION

KW - FLUIDS

KW - IONIC SYSTEMS

KW - MODEL ELECTROLYTES

KW - BOUNDARY-CONDITIONS

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DO - 10.1021/ct100365c

M3 - Article

SN - 1549-9618

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EP - 3065

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

IS - 10

ER -

A graphics processing unit implementation of Coulomb interaction in molecular dynamics

Abstract

Keywords

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