Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems

被引:52
作者
Sivak, David A. [1 ]
Chodera, John D. [2 ]
Crooks, Gavin E. [1 ]
机构
[1] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA
[2] Mem Sloan Kettering Canc Ctr, Computat Biol Program, New York, NY 10065 USA
关键词
TRANSITION; SIMULATION; ACCURACY;
D O I
10.1021/jp411770f
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon desirable properties. However, for stochastic equations of motion (e.g., Langevin dynamics), there is still broad disagreement over which integration algorithms are most appropriate. While multiple desiderata have been proposed throughout the literature, consensus on which criteria are important is absent, and no published integration scheme satisfies all desiderata simultaneously. Additional nontrivial complications stem from simulating systems driven out of equilibrium using existing stochastic integration schemes in conjunction with recently developed nonequilibrium fluctuation theorems. Here, we examine a family of discrete time integration schemes for Langevin dynamics, assessing how each member satisfies a variety of desiderata that have been enumerated in prior efforts to construct suitable Langevin integrators. We show that the incorporation of a novel time step rescaling in the deterministic updates of position and velocity can correct a number of dynamical defects in these integrators. Finally, we identify a particular splitting (related to the velocity Verlet discretization) that has essentially universally appropriate properties for the simulation of Langevin dynamics for molecular systems in equilibrium, nonequilibrium, and path sampling contexts.
引用
收藏
页码:6466 / 6474
页数:9
相关论文
共 39 条
[1]   Free energy landscape from path-sampling:: application to the structural transition in LJ38 [J].
Adjanor, G. ;
Athenes, M. ;
Calvo, F. .
EUROPEAN PHYSICAL JOURNAL B, 2006, 53 (01) :47-60
[2]   Gibbs free-energy estimates from direct path-sampling computations -: art. no. 234104 [J].
Adjanor, G ;
Athènes, M .
JOURNAL OF CHEMICAL PHYSICS, 2005, 123 (23)
[3]  
Allen M. P., 1989, Computer Simulation of Liquids, DOI DOI 10.1007/BF00646086
[5]  
[Anonymous], 1955, Rendiconti del Circolo Matematico di Palermo, DOI DOI 10.1007/BF02846028
[6]  
[Anonymous], 1997, American Journal of Physics
[7]   A path-sampling scheme for computing thermodynamic properties of a many-body system in a generalized ensemble [J].
Athènes, M .
EUROPEAN PHYSICAL JOURNAL B, 2004, 38 (04) :651-663
[8]   Measurement of nonequilibrium entropy from space-time thermodynamic integration [J].
Athenes, Manuel ;
Adjanor, Gilles .
JOURNAL OF CHEMICAL PHYSICS, 2008, 129 (02)
[9]   LONG-RUN ACCURACY OF VARIATIONAL INTEGRATORS IN THE STOCHASTIC CONTEXT [J].
Bou-Rabee, Nawaf ;
Owhadi, Houman .
SIAM JOURNAL ON NUMERICAL ANALYSIS, 2010, 48 (01) :278-297
[10]   STOCHASTIC BOUNDARY-CONDITIONS FOR MOLECULAR-DYNAMICS SIMULATIONS OF ST2 WATER [J].
BRUNGER, A ;
BROOKS, CL ;
KARPLUS, M .
CHEMICAL PHYSICS LETTERS, 1984, 105 (05) :495-500