Historical
background
Theoretical
foundations
References
Success
stories
Repository
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Historical background
Original method
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Combines three novel
ideas:
- unconstrained thermodynamic
integration
- adaptive bias based on a
local, running estimate of the free energy derivative
- a new
expression for the free energy derivative
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Andrew
Pohorille
NASA
Ames Research
Center, Moffett Field, California, and
University
of California, San Francisco, USA
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Eric
Darve
Stanford
University, Palo
Alto, California, USA
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References
- Darve, E.;
Pohorille, A. Calculating
free energies using average force,
J. Chem. Phys. 2001, 115,
9169–9183.
- Darve, E.; Wilson,
M. A.; Pohorille,
A. Calculating
free energies using a scaled-force molecular dynamics
algorithm, Mol.
Sim. 2002, 28,
113-144.
- Rodriguez-Gomez,
D.; Darve, E.;
Pohorille, A. Assessing
the efficiency of free energy calculation
methods. J.
Chem. Phys. 2004, 120,
3563-3578.
- Darve, E.; Rodriguez-Gomez,
D.; Pohorille, A. Adaptive biasing
force method for scalar and vector free energy calculations, J.
Chem. Phys. 2008, 128,
144120.
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NAMD
implementation
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Brings together
the efficiency of ABF sampling and
the
scalability of NAMD for large biomolecular simulations. Starting with NAMD 2.7,
ABF is integrated in the Collective Variables module, a flexible
framework for biased MD simulations.
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Jérôme
Hénin
LISM, CNRS and
Aix-Marseille Université, Marseille, France
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Chris
Chipot
Nancy
Université,
Vandoeuvre-lès-Nancy, France
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References
- Hénin, J.; Chipot, C. Overcoming
free energy barriers using unconstrained molecular dynamics
simulations. J. Chem. Phys. 2004, 121,
2904-2914.
- Chipot, C.; Hénin,
J. Exploring
the free-energy landscape of a short peptide using an average force.
J.
Chem. Phys. 2005, 123, 244906.
- Hénin, J.; Fiorin, J.; Chipot, C.; Klein, M.L.
Exploring Multidimensional
Free Energy Landscapes Using Time-Dependent Biases on Collective
Variables. J. Chem. Theory Comput. 2010, 6,
35-47
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Webpage
by Jérôme
Hénin and Chris
Chipot, ©2010.
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