GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP

Productivity, performance, and portability for computational fluid dynamics applications

(2020) István Z. Reguly et al.   COMPUTERS & FLUIDS

Nanobubbles diffusion in bcc uranium: Theory and atomistic modelling

(2020) Alexander Antropov et al.   JOURNAL OF NUCLEAR MATERIALS

Probing the high-pressure viscosity of hydrocarbon mixtures using molecular dynamics simulations

(2020) Nikolay D. Kondratyuk et al.   JOURNAL OF CHEMICAL PHYSICS

VASP hits the memory wall: Processors efficiency comparison

(2019) Vladimir Stegailov et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

TweTriS: Twenty trillion-atom simulation

(2019) Nikola Tchipev et al.   INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS

Formation free energies of point defects and thermal expansion of bcc U and Mo

(2019) Grigory Smirnov et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Angara interconnect makes GPU-based Desmos supercomputer an efficient tool for molecular dynamics calculations

(2019) Vladimir Stegailov et al.   INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS

More bang for your buck: Improved use of GPU nodes for GROMACS 2018

(2019) Carsten Kutzner et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Hierarchical Roofline analysis for GPUs: Accelerating performance optimization for the NERSC‐9 Perlmutter system

(2019) Charlene Yang et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

Calculation of viscosities of branched alkanes from 0.1 to 1000 MPa by molecular dynamics methods using COMPASS force field

(2019) Nikolay D. Kondratyuk et al.   FLUID PHASE EQUILIBRIA

Prediction of viscosity-density dependence of liquid methane+n-butane+n-pentane mixtures using the molecular dynamics method and empirical correlations

(2019) Vasily Pisarev et al.   FLUID PHASE EQUILIBRIA

Kokkos implementation of an Ewald Coulomb solver and analysis of performance portability

(2019) Rene Halver et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING

Implementing molecular dynamics simulation on the Sunway TaihuLight system with heterogeneous many-core processors

(2018) Wenqian Dong et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

Function portability of molecular dynamics on heterogeneous parallel architectures with OpenCL

(2018) Rene Halver et al.   JOURNAL OF SUPERCOMPUTING

Testing for physical validity in molecular simulations

(2018) Pascal T. Merz et al.   PLoS One

Dissecting GPU Memory Hierarchy Through Microbenchmarking

(2017) Xinxin Mei et al.   IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS

Optimized parallel simulations of analytic bond-order potentials on hybrid shared/distributed memory with MPI and OpenMP

(2017) Carlos Teijeiro et al.   INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

(2017) Leela S. Dodda et al.   NUCLEIC ACIDS RESEARCH

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Particle-in-Cell laser-plasma simulation on Xeon Phi coprocessors

(2016) I.A. Surmin et al.   COMPUTER PHYSICS COMMUNICATIONS

Systematic adaptation of stencil-based 3D MPDATA to GPU architectures

(2016) Krzysztof Rojek et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD

(2016) Josh V. Vermaas et al.   Journal of Chemical Information and Modeling

Self-consistent molecular dynamics calculation of diffusion in higher n-alkanes

(2016) Nikolay D. Kondratyuk et al.   JOURNAL OF CHEMICAL PHYSICS

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

(2016) Michael R. Shirts et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Performance modeling of 3D MPDATA simulations on GPU cluster

(2016) Krzysztof Rojek et al.   JOURNAL OF SUPERCOMPUTING

Nekbone performance on GPUs with OpenACC and CUDA Fortran implementations

(2016) Jing Gong et al.   JOURNAL OF SUPERCOMPUTING

Strong scaling of general-purpose molecular dynamics simulations on GPUs

(2015) Jens Glaser et al.   COMPUTER PHYSICS COMMUNICATIONS

CFD study of Jet Impingement Test erosion using Ansys Fluent ® and OpenFOAM ®

(2015) Alejandro López et al.   COMPUTER PHYSICS COMMUNICATIONS

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

(2015) Carsten Kutzner et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Kokkos: Enabling manycore performance portability through polymorphic memory access patterns

(2014) H. Carter Edwards et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING

Performance Analysis of Electronic Structure Codes on HPC Systems: A Case Study of SIESTA

(2014) Fabiano Corsetti   PLoS One

Implementing molecular dynamics on hybrid high performance computers—Three-body potentials

(2013) W. Michael Brown et al.   COMPUTER PHYSICS COMMUNICATIONS

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

MDWiZ: A platform for the automated translation of molecular dynamics simulations

(2013) Victor H. Rusu et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

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

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

Particle-in-cell plasma simulation on heterogeneous cluster systems

(2012) S. Bastrakov et al.   Journal of Computational Science

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

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

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

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

General purpose molecular dynamics simulations fully implemented on graphics processing units

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