Adaptive Biasing Force Tutorial
A tutorial for Adaptive Biasing Force (ABF) Calculations in NAMD
Jérôme Hénin and Christophe Chipot
Equipe de dynamique des assemblages membranaires
Unité Mixte de Recherche C.N.R.S./U.H.P. No 7565
Université Henri Poincaré - Nancy I
54506 Vandoeuvre-lès-Nancy, Cedex, France
March 19, 2008
This tutorial explains how NAMD and related tools can be used to setup and perform adaptive biasing force simulations to study conformational changes in biomolecular systems. The reversible unfolding of deca-alanine is used as an introductory example to demonstrate the efficiency and reversibility of the ABF method. ABF is then compared to FEP in examples to calculate the hydration free energy of methane and to demonstrate the two methods yield the same answer at a quantitative level. Finally, ABF is employed to calculate a potential of mean force for the ion pairing of sodium-chloride in water. Prior knowledge of NAMD and standard molecular dynamics simulations is assumed.
© 2006, Centre National de la Recherche Scientifique