AMBER

AMBER (an acronym for Assisted Model Building with Energy Refinement) is a family of force fields for molecular dynamics of biomolecules originally developed by Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields. It is maintained by an active collaboration between David Case at Rutgers University, Tom Cheatham at the University of Utah, Tom Darden at NIEHS, Ken Merz at Michigan State University, Carlos Simmerling at Stony Brook University, Ray Luo at UC Irvine, and Junmei Wang at Encysive Pharmaceuticals.

Force field

The term "AMBER force field" generally refers to the functional form used by the family of AMBER force fields. This form includes a number of parameters; each member of the family of AMBER force fields provides values for these parameters and has its own name.

Functional form

The functional form of the AMBER force field is

Note that despite the term force field, this equation defines the potential energy of the system; the force is the derivative of this potential with respect to position.

Waigeo language

Waigeo, also known as Ambel (Amber), is a heavily Papuan-influenced Austronesian language spoken in West Papua on the island of Waigeo, Raja Ampat islands.

References

Amber (processor core)

The Amber processor core is an open-source ARM-compatible 32-bit RISC processor. It is hosted on the OpenCores website and is part of a movement to develop a library of open source hardware intellectual property. The Amber core is fully compatible with the ARMv2 instruction set and is therefore supported by the GNU toolchain. This older version of the ARM instruction set is supported because it is not covered by patents so can be implemented without a license from ARM Holdings, unlike some previous open source projects. The Amber project provides a complete embedded FPGA system incorporating the Amber core and a number of peripherals, including UARTs, timers and an Ethernet MAC.

There are two versions of the core provided in the Amber project. The Amber 23 has a 3-stage pipeline, a unified instruction and data cache, a Wishbone interface, and is capable of 0.75 DMIPS per MHz. The Amber 25 has a 5-stage pipeline, separate data and instruction caches, a Wishbone interface, and is capable of 1.0 DMIPS per MHz. Both cores implement exactly the same ISA and are 100% software compatible.