An overview of the Amber biomolecular simulation package - WIREs
Computational Molecular Science
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An overview of the Amber biomolecular simulation package
Romelia Salomon‐Ferrer, David A. Case, Ross C. Walker
DOI: 10.1002/wcms.1121
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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
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. (C) 2012 John Wiley & Sons, Ltd.
Performance in ns/day of the Amber package version 12 on a single core AMD FX‐8120 8‐Core 3.6 GHz CPU, the Cray XT5 system and a single GPU GTX680.
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Article Title
An overview of the Amber biomolecular simulation package
Salomon‐Ferrer
Romelia, Case
David A., Walker
Ross C.. An overview of the Amber biomolecular simulation package. WIREs Comput Mol Sci 8-210. doi: 10.1002/wcms.1121Package: libapache2-mod-fcgid (1:2.3.6-1+squeeze2)
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