Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape

作者: Yuji Sugita , Yuko Okamoto

DOI: 10.1016/S0009-2614(00)00999-4

关键词:

摘要: Abstract We propose two efficient algorithms for configurational sampling of systems with rough energy landscape. The first one is a new method the determination multicanonical weight factor. In this method, short replica-exchange simulation performed and factor obtained by multiple histogram reweighting techniques. second further extension in which small number replicas. These are particularly useful studying protein folding problem.

参考文章(36)
A P Young, Spin glasses and random fields Spin Glasses and Random Fields. Edited by YOUNG A P. Published by World Scientific Publishing Co. Pte. Ltd. ,vol. 12, ,(1997) , 10.1142/3517
Denis J. Evans, G.P. Morriss, The isothermal/isobaric molecular dynamics ensemble Physics Letters A. ,vol. 98, pp. 433- 436 ,(1983) , 10.1016/0375-9601(83)90256-6
M. C. Tesi, E. J. Janse van Rensburg, E. Orlandini, S. G. Whittington, Monte carlo study of the interacting self-avoiding walk model in three dimensions Journal of Statistical Physics. ,vol. 82, pp. 155- 181 ,(1996) , 10.1007/BF02189229
Koji Nemoto, Koji Hukushima, Exchange Monte Carlo Method and Application to Spin Glass Simulations Journal of the Physical Society of Japan. ,vol. 65, pp. 1604- 1608 ,(1996) , 10.1143/JPSJ.65.1604
Christian Bartels, Martin Karplus, Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy Journal of Physical Chemistry B. ,vol. 102, pp. 865- 880 ,(1998) , 10.1021/JP972280J
Kenji Morikami, Takahisa Nakai, Akinori Kidera, Minoru Saito, Haruki Nakamura, Presto(Protein engineering simulator) : a vectorized molecular mechanics program for biopolymers Computational Biology and Chemistry. ,vol. 16, pp. 243- 248 ,(1992) , 10.1016/0097-8485(92)80010-W
Ulrich H.E. Hansmann, Yuko Okamoto, Frank Eisenmenger, Molecular dynamics, Langevin and hydrid Monte Carlo simulations in a multicanonical ensemble Chemical Physics Letters. ,vol. 259, pp. 321- 330 ,(1996) , 10.1016/0009-2614(96)00761-0
Robert H. Swendsen, Jian-Sheng Wang, Replica Monte Carlo simulation of spin glasses. Physical Review Letters. ,vol. 57, pp. 2607- 2609 ,(1986) , 10.1103/PHYSREVLETT.57.2607