Related references
Note: Only part of the references are listed.Optimized GPU implementation of Merck Molecular Force Field and Universal Force Field
Adam Jasz et al.
JOURNAL OF MOLECULAR STRUCTURE (2019)
New developments in force fields for biomolecular simulations
Paul S. Nerenberg et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)
Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks
Jing Huang et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2018)
Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: AGPU-accelerated molecular dynamics software
Lin Yang et al.
JOURNAL OF COMPUTATIONAL PHYSICS (2018)
Employing multi-GPU power for molecular dynamics simulation: an extension of GALAMOST
You-Liang Zhu et al.
MOLECULAR PHYSICS (2018)
50 million atoms scale molecular dynamics modelling on a single consumer graphics card
Gaobo Xiao et al.
ADVANCES IN ENGINEERING SOFTWARE (2018)
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features
Tai-Sung Lee et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)
Exposing Hidden Performance Opportunities in High Performance GPU Applications
Benjamin Welton et al.
2018 18TH IEEE/ACM INTERNATIONAL SYMPOSIUM ON CLUSTER, CLOUD AND GRID COMPUTING (CCGRID) (2018)
Molecular dynamics recipes for genome research
Tommaso Biagini et al.
BRIEFINGS IN BIOINFORMATICS (2018)
Reactive Molecular Dynamics on Massively Parallel Heterogeneous Architectures
Sudhir B. Kylasa et al.
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS (2017)
Toward Fast and Accurate Binding Affinity Prediction with pmemdGTl: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration
Tai-Sung Lee et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
Chigusa Kobayashi et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Peter Eastman et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
RUMD: A general purpose molecular dynamics package optimized to utilize GPU hardware down to a few thousand particles
Nicholas P. Bailey et al.
SCIPOST PHYSICS (2017)
Efficient molecular dynamics simulations with many-body potentials on graphics processing units
Zheyong Fan et al.
COMPUTER PHYSICS COMMUNICATIONS (2017)
GPU implementations of some many-body potentials for molecular dynamics simulations
Alexander S. Minkin et al.
ADVANCES IN ENGINEERING SOFTWARE (2017)
GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations
Trung Dac Nguyen
COMPUTER PHYSICS COMMUNICATIONS (2017)
An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications
Justin A. Lemkul et al.
CHEMICAL REVIEWS (2016)
Efficient neighbor list calculation for molecular simulation of colloidal systems using graphics processing units
Michael P. Howard et al.
COMPUTER PHYSICS COMMUNICATIONS (2016)
Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations
Jaewoon Jung et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Efficient implementation of the many-body Reactive Bond Order (REBO) potential on GPU
Przemyslaw Tredak et al.
JOURNAL OF COMPUTATIONAL PHYSICS (2016)
Advanced Potential Energy Surfaces for Molecular Simulation
Alex Albaugh et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
THE SEMICONDUCTOR INDUSTRY WILL SOON ABANDON ITS PURSUIT OF MOORE'S LAW. NOW THINGS COULD GET A LOT MORE INTERESTING
M. Mitchell Waldrop
NATURE (2016)
The ReaxFF reactive force-field: development, applications and future directions
Thomas P. Senftle et al.
NPJ COMPUTATIONAL MATERIALS (2016)
Strong scaling of general-purpose molecular dynamics simulations on GPUs
Jens Glaser et al.
COMPUTER PHYSICS COMMUNICATIONS (2015)
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations
Carsten Kutzner et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)
Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model
Justin A. Lemkul et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)
Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review
Eric Paquet et al.
BIOMED RESEARCH INTERNATIONAL (2015)
A Comparison between Parallelization Approaches in Molecular Dynamics Simulations on GPUs
Lorenzo Rovigatti et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)
An investigation of the effects of hard and soft errors on graphics processing unit-accelerated molecular dynamics simulations
Robin M. Betz et al.
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE (2014)
Midpoint Cell Method for Hybrid ( MPI1OpenMP) Parallelization of Molecular Dynamics Simulations
Jaewoon Jung et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)
PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs
S. B. Kylasa et al.
JOURNAL OF COMPUTATIONAL PHYSICS (2014)
Kokkos: Enabling manycore performance portability through polymorphic memory access patterns
H. Carter Edwards et al.
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING (2014)
MDGRAPE-4: a special-purpose computer system formolecular dynamics simulations
Itta Ohmura et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2014)
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
Sander Pronk et al.
BIOINFORMATICS (2013)
Petascale turbulence simulation using a highly parallel fast multipole method on GPUs
Rio Yokota et al.
COMPUTER PHYSICS COMMUNICATIONS (2013)
Molecular dynamics simulations with many-body potentials on multiple GPUs-The implementation, package and performance
Qing Hou et al.
COMPUTER PHYSICS COMMUNICATIONS (2013)
Implementing molecular dynamics on hybrid high performance computers-Three-body potentials
W. Michael Brown et al.
COMPUTER PHYSICS COMMUNICATIONS (2013)
Efficient GPU-accelerated molecular dynamics simulation of solid covalent crystals
Chaofeng Hou et al.
COMPUTER PHYSICS COMMUNICATIONS (2013)
SPFP: Speed without compromise-A mixed precision model for GPU accelerated molecular dynamics simulations
Scott Le Grand et al.
COMPUTER PHYSICS COMMUNICATIONS (2013)
A flexible algorithm for calculating pair interactions on SIMD architectures
Szilard Pall et al.
COMPUTER PHYSICS COMMUNICATIONS (2013)
Accelerated molecular dynamics force evaluation on graphics processing units for thermal conductivity calculations
Zheyong Fan et al.
COMPUTER PHYSICS COMMUNICATIONS (2013)
GPU-Enabled Macromolecular Simulation: Challenges and Opportunities
Michela Taufer et al.
COMPUTING IN SCIENCE & ENGINEERING (2013)
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
Peter Eastman et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
Pedro E. M. Lopes et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins
Yue Shi et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
Romelia Salomon-Ferrer et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
GALAMOST: GPU-accelerated large-scale molecular simulation toolkit
You-Liang Zhu et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)
GPU-accelerated molecular mechanics computations
Athanasios Anthopoulos et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)
Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics
Mo Zheng et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2013)
Graphics processing unit (GPU) programming strategies and trends in GPU computing
Andre R. Brodtkorb et al.
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING (2013)
A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids
Janamejaya Chowdhary et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
Efficient parallelization of short-range molecular dynamics simulations on many-core systems
R. Meyer
PHYSICAL REVIEW E (2013)
An overview of the Amber biomolecular simulation package
Romelia Salomon-Ferrer et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2013)
Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation
Nathan Schmid et al.
COMPUTER PHYSICS COMMUNICATIONS (2012)
Implementing molecular dynamics on hybrid high performance computers - Particle-particle particle-mesh
W. Michael Brown et al.
COMPUTER PHYSICS COMMUNICATIONS (2012)
Sequence-dependent thermodynamics of a coarse-grained DNA model
Petr Sulc et al.
JOURNAL OF CHEMICAL PHYSICS (2012)
GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations
David E. Tanner et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
Andreas W. Goetz et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
GPU-accelerated molecular dynamics simulation of solid covalent crystals
Chaofeng Hou et al.
MOLECULAR SIMULATION (2012)
Computational aspects of many-body potentials
Steven J. Plimpton et al.
MRS BULLETIN (2012)
Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques
H. M. Aktulga et al.
PARALLEL COMPUTING (2012)
Recent developments and applications of the CHARMM force fields
Xiao Zhu et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2012)
A survey of computational molecular science using graphics processing units
M. J. Harvey et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2012)
Parallel Molecular Dynamics with Irregular Domain Decomposition
Mauro Bisson et al.
COMMUNICATIONS IN COMPUTATIONAL PHYSICS (2011)
Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs
I. V. Morozov et al.
COMPUTER PHYSICS COMMUNICATIONS (2011)
Enhanced molecular dynamics performance with a programmable graphics processor
D. C. Rapaport
COMPUTER PHYSICS COMMUNICATIONS (2011)
Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUS and a billion unknowns
Rio Yokota et al.
COMPUTER PHYSICS COMMUNICATIONS (2011)
Highly accelerated simulations of glassy dynamics using GPUs: Caveats on limited floating-point precision
Peter H. Colberg et al.
COMPUTER PHYSICS COMMUNICATIONS (2011)
Rigid body constraints realized in massively-parallel molecular dynamics on graphics processing units
Trung Dac Nguyen et al.
COMPUTER PHYSICS COMMUNICATIONS (2011)
Implementing molecular dynamics on hybrid high performance computers - short range forces
W. Michael Brown et al.
COMPUTER PHYSICS COMMUNICATIONS (2011)
MOIL-opt: Energy-Conserving Molecular Dynamics on a GPU/CPU System
A. Peter Ruymgaart et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Molecular Dynamics Simulations of Aqueous Ions at the Liquid-Vapor Interface Accelerated Using Graphics Processors
Brad A. Bauer et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
Molecular Dynamics Simulations Using Graphics Processing Units
John A. Baker et al.
MOLECULAR INFORMATICS (2011)
GROMACS-the road ahead
David van der Spoel et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2011)
Accelerating Molecular Dynamics Simulation Using Graphics Processing Unit
Hun Joo Myung et al.
BULLETIN OF THE KOREAN CHEMICAL SOCIETY (2010)
OpenMM: A Hardware-Independent Framework for Molecular Simulations
Peter Eastman et al.
COMPUTING IN SCIENCE & ENGINEERING (2010)
THE GPU COMPUTING ERA
John Nickolls et al.
IEEE MICRO (2010)
High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing
I. Buch et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)
A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics
Prateek K. Jha et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Current Status of the AMOEBA Polarizable Force Field
Jay W. Ponder et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Molecular dynamics simulation of macromolecules using graphics processing unit
Ji Xu et al.
MOLECULAR SIMULATION (2010)
SOP-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors
A. Zhmurov et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
M. J. Harvey et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware
M. J. Harvey et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Accelerating Molecular Dynamic Simulation on Graphics Processing Units
Mark S. Friedrichs et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
Multilevel summation of electrostatic potentials using graphics processing units
David J. Hardy et al.
PARALLEL COMPUTING (2009)
Anton, a special-purpose machine for molecular dynamics simulation
David E. Shaw et al.
COMMUNICATIONS OF THE ACM (2008)
Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA
Weiguo Liu et al.
COMPUTER PHYSICS COMMUNICATIONS (2008)
Parallel computing experiences with CUDA
Michael Garland et al.
IEEE MICRO (2008)
De novo ultrascale atomistic simulations on high-end parallel supercomputers
Aiichiro Nakano et al.
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS (2008)
Fast multipole methods on graphics processors
Nail A. Gumerov et al.
JOURNAL OF COMPUTATIONAL PHYSICS (2008)
General purpose molecular dynamics simulations fully implemented on graphics processing units
Joshua A. Anderson et al.
JOURNAL OF COMPUTATIONAL PHYSICS (2008)
Harvesting graphics power for MD simulations
J. A. van Meel et al.
MOLECULAR SIMULATION (2008)
Accelerating molecular modeling applications with graphics processors
John E. Stone et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2007)
Performance of the Cell processor for biomolecular simulations
G. De Fabritiis
COMPUTER PHYSICS COMMUNICATIONS (2007)
GPU accelerated molecular dynamics simulation of thermal conductivities
Juekuan Yang et al.
JOURNAL OF COMPUTATIONAL PHYSICS (2007)
Comparison of multiple amber force fields and development of improved protein backbone parameters
Viktor Hornak et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins
Changbong Hyeon et al.
STRUCTURE (2006)
Accelerating molecular dynamics simulations with configurable circuits
Y. Gu et al.
IEE PROCEEDINGS-COMPUTERS AND DIGITAL TECHNIQUES (2006)
Parallelizing a molecular dynamics algorithm on a multiprocessor workstation using OpenMP
KB Tarmyshov et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2005)
Brook for GPUs: Stream computing on graphics hardware
I Buck et al.
ACM TRANSACTIONS ON GRAPHICS (2004)
Improved neighbor list algorithm in molecular simulations using cell decomposition and data sorting method
ZH Yao et al.
COMPUTER PHYSICS COMMUNICATIONS (2004)
Empirical force fields for biological macromolecules: Overview and issues
AD Mackerell
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Hardware accelerator for molecular dynamics: MDGRAPE-2
R Susukita et al.
COMPUTER PHYSICS COMMUNICATIONS (2003)
A simple polarizable model of water based on classical Drude oscillators
G Lamoureux et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Cg: A system for programming graphics hardware in a C-like language
WR Mark et al.
ACM TRANSACTIONS ON GRAPHICS (2003)
Polarizable atomic multipole water model for molecular mechanics simulation
PY Ren et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2003)
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations
PY Ren et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
Exploiting multiple levels of parallelism in Molecular Dynamics based calculations via modern techniques and software paradigms on distributed memory computers
ME Tuckerman et al.
COMPUTER PHYSICS COMMUNICATIONS (2000)
Share Paper
