Transition path sampling of rare events by shooting from the top

被引:45
作者
Jung, Hendrik [1 ,2 ]
Okazaki, Kei-ichi [1 ,3 ]
Hummer, Gerhard [1 ,4 ]
机构
[1] Max Planck Inst Biophys, Dept Theoret Biophys, Max von Laue Str 3, D-60438 Frankfurt, Germany
[2] Goethe Univ Frankfurt, Dept Phys, D-60438 Frankfurt, Germany
[3] Natl Inst Nat Sci, Inst Mol Sci, Dept Theoret & Computat Mol Sci, Okazaki, Aichi 4448585, Japan
[4] Goethe Univ Frankfurt, Inst Biophys, D-60438 Frankfurt, Germany
关键词
RATE-CONSTANT; ASSOCIATION; SIMULATION; DYNAMICS;
D O I
10.1063/1.4997378
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
Transition path sampling is a powerful tool in the study of rare events. Shooting trial trajectories from configurations along existing transition paths proved particularly efficient in the sampling of reactive trajectories. However, most shooting attempts tend not to result in transition paths, in particular in cases where the transition dynamics has diffusive character. To overcome the resulting efficiency problem, we developed an algorithm for "shooting from the top." We first define a shooting range through which all paths have to pass and then shoot off trial trajectories only from within this range. For a well chosen shooting range, nearly every shot is successful, resulting in an accepted transition path. To deal with multiple mechanisms, weighted shooting ranges can be used. To cope with the problem of unsuitably placed shooting ranges, we developed an algorithm that iteratively improves the location of the shooting range. The transition path sampling procedure is illustrated for models of diffusive and Langevin dynamics. The method should be particularly useful in cases where the transition paths are long so that only relatively few shots are possible, yet reasonable order parameters are known. (C) 2017 Author(s).
引用
收藏
页数:10
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