Host Dynamics under General-Purpose Force Fields

General-Purpose Computation without General-Purpose Processors

Force fields and molecular dynamics simulations

The objective of this review is to serve as an introductory guide for the non-expert to the exciting field of Molecular Dynamics (MD). MD simulations generate a phase space trajectory by integrating the classical equations of motion for a system of N particles. Here I review the basic concepts needed to understand the technique, what are the key elements to perform a simulation and which is the...

Strong scaling of general-purpose molecular dynamics simulations on GPUs

Wedescribe a highly optimized implementation ofMPI domain decomposition in aGPU-enabled, generalpurpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, 2013). Our approach is inspired by a traditional CPU-based code, LAMMPS (Plimpton, 1995), but is implemented within a code that was designed for execution on GPUs from the start (Anderson et al., 2008). The software supports shortrang...

General-purpose molecular dynamics simulations on GPU-based clusters

We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables multi-GPU simulation on hybrid heterogeneous clusters, using MPI for inter-node communication, CUDA kernels on the GPU for all methods working with particle data, a...

General Purpose Work Flow Languages General Purpose Work Flow Languages *

Work ow management requires language support for work ow speciication and task speciication. Many approaches and systems for work ow managementtherefore ooer at least one new language for work ow speciication; task speciication is usually done in a traditional language. This is motivated in particular by the fact that many components already exist and the task of the work ow tool is the speciic...