ENHANCED SAMPLING OF MULTIDIMENSIONAL FREE-ENERGY LANDSCAPES USING ADAPTIVE BIASING FORCES

被引:25
作者
Chipot, Christophe [1 ]
Lelievre, Tony [2 ,3 ]
机构
[1] Nancy Univ, UMR 7565, Equipe Dynam Assemblages Membranaires, F-54506 Vandoeuvre Les Nancy, France
[2] Univ Paris Est, CERMICS, F-77455 Marne La Vallee, France
[3] Ecole Ponts ParisTech, INRIA, MICMAC Project Team, F-77455 Marne La Vallee, France
关键词
nonlinear Fokker-Planck equation; long-time behavior; entropy techniques; adaptive biasing force; CYCLIC PEPTIDE NANOTUBE; LOGARITHMIC SOBOLEV INEQUALITIES; MOLECULAR-DYNAMICS SIMULATIONS; ASSEMBLING ORGANIC NANOTUBES; ALANINE DIPEPTIDE; CONFORMATIONAL TRANSITIONS; AQUEOUS-SOLUTION; ALA DIPEPTIDE; MEAN FORCE; GAS-PHASE;
D O I
10.1137/10080600X
中图分类号
O29 [应用数学];
学科分类号
070104 ;
摘要
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.
引用
收藏
页码:1673 / 1695
页数:23
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