We assess the progress in biomolecular modeling and simulation, focusing on structure
prediction and dynamics, by presenting the field's history, metrics for its rise in popularity …

NAMD is a parallel molecular dynamics code designed for high‐performance simulation of
large biomolecular systems. NAMD scales to hundreds of processors on high‐end parallel …

Although molecular dynamics (MD) simulations of biomolecular systems often run for days to
months, many events of great scientific interest and pharmaceutical relevance occur on long …

The high arithmetic performance and intrinsic parallelism of recent graphical processing
units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is …

Anton is a recently completed special-purpose supercomputer designed for molecular
dynamics (MD) simulations of biomolecular systems. The machine's specialized hardware …

The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins
and other biological macro-molecules could in principle provide answers to some of the …

We are developing the MDGRAPE-4, a special-purpose computer system for molecular
dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for …

A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom
biological systems on massively parallel supercomputers. The strategy is developed using …

Molecular Dynamics applications enhance our understanding of biological phenomena
through bio-molecular simulations. Large-scale parallelization of MD simulations is …

This book highlights the use of Charm++ in a wide variety of scientific and engineering
fields. It emphasizes the adaptivity, asynchrony, and message-driven execution of Charm++ …