Amber developers, October, 2004
Amber is the collective name for a suite of programs that allow users to
carry out molecular dynamics simulations, particularly on biomolecules. None
of the individual programs carries this name, but the various parts
work reasonably well together, and provide a powerful framework for many
common calculations. The term amber is also sometimes used to refer
to the empirical force field that is implemented here. It should be
recognized however, that the code and force field are separate: several other
computer packages have implemented the amber force field, and
other force fields can be implemented with the amber programs. Further,
the force field is in the public domain, whereas the codes are distributed
under a license agreement.
The best overview of AMBER is in the following paper: D.A. Pearlman, D.A.
Case, J.W. Caldwell, W.R. Ross, T.E. Cheatham, III,
S. DeBolt, D. Ferguson, G. Seibel
and P. Kollman. AMBER, a computer program for applying molecular mechanics,
normal mode analysis, molecular dynamics and free energy calculations to
elucidate the structures and energies of molecules. Computer Physics
Communications 91, 1-41 (1995).
The most recent version of AMBER is version 10, released in April, 2006.
The key new features are listed here:
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Force fields: Many new force field types are available, including
new water and ion models; updated nucleic acid and carbohydrate parameters;
parallel support for the AMOEBA polarizable potentials of Ren and Ponder; and
improved empirical valence bond (EVB) models that can be used to construct
approximate potentials for chemical reactions.
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QM/MM Simulations: Amber 10 now allows DFTB calculations in periodic
solvent boxes or with the generalized Born solvation model. Codes are faster
and (modestly) parallel.
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Adaptively biased simulations can be used to accelerate sampling and free
energy convergence.
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Path integral molecular dynamics simulations can be used to sample
equilibrium canonical distributions using quantum dynamics rather than
Newton's equations for nuclear motion. Both equilibrium and kinetic isotope
effects can be estimated via thermodynamic integration over mass. Rate
constants can be estimated using the Quantum Instanton model, and approximate
quantum time-correlation functions are available using Ring Polymer MD or
Centroid MD.
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A new suite of conformational clustering tools is available in ptraj.
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New free energy tools significantly simplify the setup of mutational
changes in proteins, allowing for both "single" and "dual" topologies.
A soft-core potential facility aids
sampling in systems where atoms are appearing or disappearing, with no need
for the creation of artificial dummy atoms.
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Updates to the replica exchange methods, including improvements to
the standard replica exchange code and support for exchange methods with a
non-Boltzmann reservoir, or in which a hybrid solvent model is used to reduce
the number of replicas required for large systems in explicit solvent.
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Significant improvements in speed and parallel scaling are available
in an expanded pmemd program, which now includes generalized Born
capability, and support for off-center charges (as in TIP4P or TIP5P).
- Full integration of the low-mode (LMOD) search tools based on
following low-frequency normal modes.
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D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J.
Wang, R.E. Duke, R. Luo, M. Crowley, R.C. Walker, W. Zhang, K.M.
Merz, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossváry, K.F.
Wong, F. Paesani, J. Vanicek, X. Wu, S.R. Brozell, T. Steinbrecher, H.
Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D.H.
Mathews, M.G. Seetin, C. Sagui, V. Babin, and P.A. Kollman
The most complete and up-to-date information (including instructions on
obtaining AMBER) is maintained here:
http://ambermd.org
Updated on April 17, 2008. Comments to case@scripps.edu