AMBER (Assisted Model Building with Energy Refinement) refers to a suite of programs (http://ambermd.org/) for molecular dynamics simulations of proteins and nucleic acids. The package includes a number of useful programs that allow the preparation of necessary input files, setup and perform molecular dynamics simulations and analysis of the final results from MD simulations. It is one of the most widely used programs for biomolecular studies and has an efficient parallel scaling implementation. The name Amber also refers to a set of molecular mechanics force fields for the simulation of biomolecules.

 

Application/Keywords: Molecular Dynamics Simulations, Energy Minimization, Quantum Mechanics, Implicit water, GPU acceleration, Enhanced Sampling