An overview of the Amber biomolecular simulation package

TLDR

Molecular dynamics enables atomistic study of biological and chemical systems, complements experiments, and is supported by many software packages, with Amber being one of the most widely used. The authors aim to outline recent developments in Amber and AmberTools and provide a condensed vision of current capabilities and future directions. They review the latest developments of Amber and AmberTools, describing the software’s evolution and current features. Version 12 of Amber, released in 2012, introduces significant scientific and computational advances and demonstrates strong performance, achieving high ns/day on CPUs and GPUs. © 2012 John Wiley & Sons, Ltd.

Abstract

Abstract Molecular dynamics (MD) allows the study of biological and chemical systems at the atomistic level on timescales from femtoseconds to milliseconds. It complements experiment while also offering a way to follow processes difficult to discern with experimental techniques. Numerous software packages exist for conducting MD simulations of which one of the widest used is termed Amber. Here, we outline the most recent developments, since version 9 was released in April 2006, of the Amber and AmberTools MD software packages, referred to here as simply the Amber package. The latest release represents six years of continued development, since version 9, by multiple research groups and the culmination of over 33 years of work beginning with the first version in 1979. The latest release of the Amber package, version 12 released in April 2012, includes a substantial number of important developments in both the scientific and computer science arenas. We present here a condensed vision of what Amber currently supports and where things are likely to head over the coming years. Figure 1 shows the performance in ns/day of the Amber package version 12 on a single‐core AMD FX‐8120 8‐Core 3.6GHz CPU, the Cray XT5 system, and a single GPU GTX680. © 2012 John Wiley & Sons, Ltd. This article is categorized under: Software > Molecular Modeling