Amber/AmberTools
Overview
Amber and AmberTools are a suite of biomolecular simulation programs. It began in the late 1970’s, and is maintained by an active development community; see the history page and the contributors page for more information.
The term “Amber” refers to two things. First, it is a set of molecular mechanical force fields for the simulation of biomolecules (these force fields are in the public domain, and are used in a variety of simulation programs). Second, it is a package of molecular simulation programs which includes source code and demos.
AmberTools are open-source while Amber (pmemd) requires a license.
Amber implements efficient simulations with periodic boundary conditions, using the PME method for electrostatic interactions and a continuum model for long-range van der Waals interactions. […] Explicit support is provided for carbohydrate simulations, as well as for proteins, nucleic acids and small organic molecules.
Case et al, The Amber biomolecular simulation programs, J. Comput. Chem.. 2005, 26, 1668-1688. https://doi.org/10.1002/jcc.20290
Core Methods
Users at FAU
- Computational Biology (Prof. Rainer Böckmann)
- Computer Chemistry Center (Prof. Tim Clark, Prof. Petra Imhof)
- Bioinformatics (Prof. Heinrich Sticht)
- Physics Underlying Life Science (PULS) Group (Prof. Ana-Sunčana Smith)
Developers at FAU
- no core developers at FAU