非连续分子动力学模拟方法及其在大分子研究中的应用

Discontinuous Molecular Dynamics Simulation and Its Applications in Macromolecular Studies

计算机模拟技术已成为大分子构象等基础研究的一种重要手段。非连续分子动力学模拟(DMD)与传统的分子动力学模拟(MD)方法有所不同,基于不连续势能和相关的模拟编程方法,运行速度大大提高。本文讨论了DMD方法的特点,总结了DMD方法的应用,重点以蛋白质折叠为例介绍了如何使用DMD方法,最后对DMD方法的发展前景进行了展望。

Computer simulations have become one of critical tools to study fundamental problems related to macromolecular conformations. Different from conventional molecular dynamics simulation, discontinuous molecular dynamics （DMD） simulation is based upon a discontinuous potential and unique programming skills, and thus saves computing cost greatly. This review summarizes the advantages, limitations and applications of DMD. With protein folding as an example, the review demonstrates how to use the DMD method to resolve scientific problems. Finally, a brief prospect is presented.