Byrne D, Li J, Platt E, Robson B, Weiner P
Proteus Molecular Design Ltd., Macclesfield, Cheshire, U.K.
J Comput Aided Mol Des. 1994 Feb;8(1):67-82. doi: 10.1007/BF00124350.
The modelling of biological molecules by molecular dynamics is beset by a range of problems. The most important of these is the multiple-minima problem. The deep metastable minima can cause difficulties in proper equilibration of a molecular system and result in the simulated system being trapped in a long-lived metastable state. One way to overcome these problems is to re-engineer the 'Newtonian Rules' in order to more efficiently search conformational space. Re-engineering of the 'Newtonian Rules' implies a redesign of the physical laws arising from them. This is done in various ways by the RUSH, Hybrid Monte Carlo and PEACS algorithms. This paper explores applications of these algorithms, and compares them to a traditional molecular dynamics method.
通过分子动力学对生物分子进行建模面临一系列问题。其中最重要的是多极小值问题。深度亚稳态极小值会给分子系统的适当平衡带来困难，并导致模拟系统被困在长寿命亚稳态。克服这些问题的一种方法是重新设计“牛顿规则”，以便更有效地搜索构象空间。重新设计“牛顿规则”意味着重新设计由它们产生的物理定律。RUSH、混合蒙特卡罗和PEACS算法通过各种方式实现这一点。本文探讨了这些算法的应用，并将它们与传统分子动力学方法进行了比较。
