Algorithms for GPU-based molecular dynamics simulations of complex fluids: Applications to water, mixtures, and liquid crystals

Strong scaling of general-purpose molecular dynamics simulations on GPUs

(2015) Jens Glaser et al.   COMPUTER PHYSICS COMMUNICATIONS

Advancing simulations of biological materials: applications of coarse-grained models on graphics processing unit hardware

(2014) David N. LeBard   MOLECULAR SIMULATION

A flexible algorithm for calculating pair interactions on SIMD architectures

(2013) Szilárd Páll et al.   COMPUTER PHYSICS COMMUNICATIONS

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

GPU-accelerated molecular mechanics computations

(2013) Athanasios Anthopoulos et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

2012 Freeman Scholar Lecture: Computational Fluid Dynamics on Graphics Processing Units

(2013) S. P. Vanka   JOURNAL OF FLUIDS ENGINEERING-TRANSACTIONS OF THE ASME

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Manipulation of Liquid Crystals by an Orienting Force in MD Simulations

(2012) Christopher D. Daub et al.   FERROELECTRICS

Atomistic simulations of liquid crystal mixtures of alkoxy substituted phenylpyrimidines 2PhP and PhP14

(2012) Fangyong Yan et al.   JOURNAL OF CHEMICAL PHYSICS

Revisiting Molecular Dynamics on a CPU/GPU System: Water Kernel and SHAKE Parallelization

(2012) A. Peter Ruymgaart et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Acceleration of coarse grain molecular dynamics on GPU architectures

(2012) Ardita Shkurti et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

An optimized approach to histogram computation on GPU

(2012) Juan Gómez-Luna et al.   MACHINE VISION AND APPLICATIONS

A survey of computational molecular science using graphics processing units

(2012) M. J. Harvey et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Highly accelerated simulations of glassy dynamics using GPUs: Caveats on limited floating-point precision

(2011) Peter H. Colberg et al.   COMPUTER PHYSICS COMMUNICATIONS

Implementing molecular dynamics on hybrid high performance computers – Particle–particle particle-mesh

(2011) W. Michael Brown et al.   COMPUTER PHYSICS COMMUNICATIONS

SHAKE parallelization

(2011) R. Elber et al.   European Physical Journal-Special Topics

Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics

(2011) Benjamin G. Levine et al.   Journal of Chemical Theory and Computation

Fast analysis of molecular dynamics trajectories with graphics processing units—Radial distribution function histogramming

(2011) Benjamin G. Levine et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Implementing molecular dynamics on hybrid high performance computers – short range forces

(2010) W. Michael Brown et al.   COMPUTER PHYSICS COMMUNICATIONS

Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulations

(2010) Peter Eastman et al.   Journal of Chemical Theory and Computation

GPU-accelerated molecular dynamics simulation for study of liquid crystalline flows

(2010) Alfeus Sunarso et al.   JOURNAL OF COMPUTATIONAL PHYSICS

GPU-accelerated molecular modeling coming of age

(2010) John E. Stone et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

A molecular dynamics study of chirality transfer from chiral surfaces to nearby solvent

(2009) Shihao Wang et al.   JOURNAL OF CHEMICAL PHYSICS

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

General purpose molecular dynamics simulations fully implemented on graphics processing units

(2008) Joshua A. Anderson et al.   JOURNAL OF COMPUTATIONAL PHYSICS

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation