Paper Citing NAMD - Abstract
Chipot, Christophe; Lelievre, Tony
ENHANCED SAMPLING OF MULTIDIMENSIONAL FREE-ENERGY LANDSCAPES USING ADAPTIVE BIASING FORCES
SIAM JOURNAL ON APPLIED MATHEMATICS, 71:1673-1695, 2011
We propose an adaptive biasing algorithm aimed at enhancing the sampling of multimodal measures by Langevin dynamics. The underlying idea consists in generalizing the standard adaptive biasing force method commonly used in conjunction with molecular dynamics to handle in a more effective fashion multidimensional reaction coordinates. The proposed approach is anticipated to be particularly useful for reaction coordinates, the components of which are weakly coupled, as illuminated in a mathematical analysis of the long-time convergence of the algorithm. The strength as well as the intrinsic limitation of the method are discussed and illustrated in two realistic test cases.
