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An overview of the Amber biomolecular simulation package

Salomon‐Ferrer, Romelia, Case, David A., Walker, Ross C.·2013·WIREs Computational Molecular Science
DOI 10.1002/wcms.1121
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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

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Metadata

Authors
Salomon‐Ferrer, R., Case, D. A., & Walker, R. C.
Venue
WIREs Computational Molecular Science
Publisher
Wiley
Published
2012-09-25
Volume
3
Issue
2
Pages
198-210
ISSN
  • 1759-0876 (ISSN-L)
  • 1759-0884
DOI
10.1002/wcms.1121
OpenAlex
W2103325328
Cited by
2,623
References
1
FWCI
24.74
Type
journal article
Language
en
Open access
closed
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor)

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