[HTML][HTML] Classical and reactive molecular dynamics: Principles and applications in combustion and energy systems
Molecular dynamics (MD) has evolved into a ubiquitous, versatile and powerful
computational method for fundamental research in science branches such as biology …
computational method for fundamental research in science branches such as biology …
A survey of CPU-GPU heterogeneous computing techniques
As both CPUs and GPUs become employed in a wide range of applications, it has been
acknowledged that both of these Processing Units (PUs) have their unique features and …
acknowledged that both of these Processing Units (PUs) have their unique features and …
Implementing molecular dynamics on hybrid high performance computers–short range forces
The use of accelerators such as graphics processing units (GPUs) has become popular in
scientific computing applications due to their low cost, impressive floating-point capabilities …
scientific computing applications due to their low cost, impressive floating-point capabilities …
Implementing molecular dynamics on hybrid high performance computers–Particle–particle particle-mesh
The use of accelerators such as graphics processing units (GPUs) has become popular in
scientific computing applications due to their low cost, impressive floating-point capabilities …
scientific computing applications due to their low cost, impressive floating-point capabilities …
GPU-accelerated molecular modeling coming of age
Graphics processing units (GPUs) have traditionally been used in molecular modeling solely
for visualization of molecular structures and animation of trajectories resulting from …
for visualization of molecular structures and animation of trajectories resulting from …
Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for …
The calculation of a protein-ligand binding free energy based on molecular dynamics (MD)
simulations generally relies on a thermodynamic cycle in which the ligand is alchemically …
simulations generally relies on a thermodynamic cycle in which the ligand is alchemically …
Assembly of finite element methods on graphics processors
Recently, graphics processing units (GPUs) have had great success in accelerating many
numerical computations. We present their application to computations on unstructured …
numerical computations. We present their application to computations on unstructured …
Free energy methods in drug discovery—introduction
Complete understanding of most, if not all chemical processes requires at its very core the
knowledge of the underlying free-energy change. In computer-aided drug design, for …
knowledge of the underlying free-energy change. In computer-aided drug design, for …
[HTML][HTML] The u-series: A separable decomposition for electrostatics computation with improved accuracy
The evaluation of electrostatic energy for a set of point charges in a periodic lattice is a
computationally expensive part of molecular dynamics simulations (and other applications) …
computationally expensive part of molecular dynamics simulations (and other applications) …
Design, parameterization, and implementation of atomic force fields for adsorption in nanoporous materials
Molecular simulations are an excellent tool to study adsorption and diffusion in nanoporous
materials. Examples of nanoporous materials are zeolites, carbon nanotubes, clays, metal …
materials. Examples of nanoporous materials are zeolites, carbon nanotubes, clays, metal …