Paper Citing NAMD - Abstract
Xu, Dong; Williamson, Mark J.; Walker, Ross C.
Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units
ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY, VOL 6, 6:3-19, 2010
Over the past few years competition within the computer game market coupled with the emergence of application programming interfaces to support general purpose computation on graphics processing units (GPUs) has led to an explosion in the use of GPUs for acceleration of scientific applications. Here we explore the use of GPUs within the context of condensed phase molecular dynamics (MD) simulations. We discuss the algorithmic differences that the GPU architecture imposes on MD codes, an overview of the challenges involved in using GPUs for MD, followed by a critical survey of contemporary MD simulation packages that are attempting to utilize GPUs. Finally we discuss the possible outlook for this field.
