Transition path sampling on diffusive barriers

被引:61
作者
Bolhuis, PG [1 ]
机构
[1] Univ Amsterdam, Dept Chem Engn, NL-1018 WV Amsterdam, Netherlands
关键词
D O I
10.1088/0953-8984/15/1/314
中图分类号
O469 [凝聚态物理学];
学科分类号
070205 ;
摘要
We have adapted the transition path sampling algorithm for the study of activated diffusive processes in complex systems, in which the system has to overcome a high and rough free energy barrier. The new scheme is based on the stochastic shooting procedure and employs molecular dynamics trajectories with an Andersen thermostat as a noise generator. The algorithm is illustrated on a diffusive process in a dense Lennard-Jones fluid.
引用
收藏
页码:S113 / S120
页数:8
相关论文
共 15 条
[1]   MOLECULAR-DYNAMICS SIMULATIONS AT CONSTANT PRESSURE AND-OR TEMPERATURE [J].
ANDERSEN, HC .
JOURNAL OF CHEMICAL PHYSICS, 1980, 72 (04) :2384-2393
[2]   Transition path sampling: Throwing ropes over rough mountain passes, in the dark [J].
Bolhuis, PG ;
Chandler, D ;
Dellago, C ;
Geissler, PL .
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, 2002, 53 :291-318
[3]   Sampling ensembles of deterministic transition pathways [J].
Bolhuis, PG ;
Dellago, C ;
Chandler, D .
FARADAY DISCUSSIONS, 1998, 110 :421-436
[4]  
BOLHUIS PG, 2002, IN PRESS
[5]   On the calculation of reaction rate constants in the transition path ensemble [J].
Dellago, C ;
Bolhuis, PG ;
Chandler, D .
JOURNAL OF CHEMICAL PHYSICS, 1999, 110 (14) :6617-6625
[6]   Transition path sampling and the calculation of rate constants [J].
Dellago, C ;
Bolhuis, PG ;
Csajka, FS ;
Chandler, D .
JOURNAL OF CHEMICAL PHYSICS, 1998, 108 (05) :1964-1977
[7]   Transition path sampling [J].
Dellago, C ;
Bolhuis, PG ;
Geissler, PL .
ADVANCES IN CHEMICAL PHYSICS, VOL 123, 2002, 123 :1-78
[8]   Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements [J].
Dellago, C ;
Bolhuis, PG ;
Chandler, D .
JOURNAL OF CHEMICAL PHYSICS, 1998, 108 (22) :9236-9245
[9]   Simulation of protein folding by reaction path annealing [J].
Eastman, P ;
Gronbech-Jensen, N ;
Doniach, S .
JOURNAL OF CHEMICAL PHYSICS, 2001, 114 (08) :3823-3841
[10]   Stochastic path approach to compute atomically detailed trajectories: Application to the folding of C peptide [J].
Elber, R ;
Meller, J ;
Olender, R .
JOURNAL OF PHYSICAL CHEMISTRY B, 1999, 103 (06) :899-911