LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
Since the classical molecular dynamics simulator LAMMPS was released as an open source
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …
Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald
We present an implementation of explicit solvent all atom classical molecular dynamics (MD)
within the AMBER program package that runs entirely on CUDA-enabled GPUs. First …
within the AMBER program package that runs entirely on CUDA-enabled GPUs. First …
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian
genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing …
genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing …
Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized born
We present an implementation of generalized Born implicit solvent all-atom classical
molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA …
molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA …
Tackling exascale software challenges in molecular dynamics simulations with GROMACS
GROMACS is a widely used package for biomolecular simulation, and over the last two
decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration …
decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration …
SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations
A new precision model is proposed for the acceleration of all-atom classical molecular
dynamics (MD) simulations on graphics processing units (GPUs). This precision model …
dynamics (MD) simulations on graphics processing units (GPUs). This precision model …
Strong scaling of general-purpose molecular dynamics simulations on GPUs
We describe a highly optimized implementation of MPI domain decomposition in a GPU-
enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer …
enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer …
A flexible algorithm for calculating pair interactions on SIMD architectures
Calculating interactions or correlations between pairs of particles is typically the most time-
consuming task in particle simulation or correlation analysis. Straightforward …
consuming task in particle simulation or correlation analysis. Straightforward …
Discrete simulation of granular and particle-fluid flows: from fundamental study to engineering application
Multiphase chemical reactors with characteristic multiscale structures are intrinsically
discrete at the elemental scale. However, due to the lack of multiscale models and the …
discrete at the elemental scale. However, due to the lack of multiscale models and the …
Meeting the contact-mechanics challenge
This paper summarizes the submissions to a recently announced contact-mechanics
modeling challenge. The task was to solve a typical, albeit mathematically fully defined …
modeling challenge. The task was to solve a typical, albeit mathematically fully defined …