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adaptive biasing force
 
Overcoming free energy barriers in molecular simulations using an average force
 


Historical background

Theoretical foundations
References
Success stories
Repository
Contact us


Historical background



Original method


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





Andrew Pohorille

NASA Ames Research Center, Moffett Field, California, and
University of California, San Francisco, USA






Eric Darve

Stanford University, Palo Alto, California, USA


References

  1. Darve, E.; Pohorille, A. Calculating free energies using average force, J. Chem. Phys. 2001, 115, 9169–9183.
  2. Darve, E.; Wilson, M. A.; Pohorille, A. Calculating free energies using a scaled-force molecular dynamics algorithm, Mol. Sim. 2002, 28, 113-144.
  3. Rodriguez-Gomez, D.; Darve, E.; Pohorille, A. Assessing the efficiency of free energy calculation methods. J. Chem. Phys. 2004, 120, 3563-3578.
  4. Darve, E.; Rodriguez-Gomez, D.; Pohorille, A. Adaptive biasing force method for scalar and vector free energy calculations, J. Chem. Phys. 2008, 128, 144120.



NAMD implementation


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.





Jérôme Hénin

LISM, CNRS and Aix-Marseille Université, Marseille, France





Chris Chipot

Nancy Université, Vandoeuvre-lès-Nancy, France



References

  1. Hénin, J.; Chipot, C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J. Chem. Phys. 2004, 121, 2904-2914.
  2. Chipot, C.; Hénin, J. Exploring the free-energy landscape of a short peptide using an average force. J. Chem. Phys. 2005, 123, 244906.
  3. 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.