Torras Juan, Roberts Benjamin P, Seabra Gustavo M, Trickey Samuel B
Department of Chemical Engineering, EEI, Universitat Politècnica de Catalunya, Igualada, Spain.
Centre for eResearch, The University of Auckland, Auckland, New Zealand.
Adv Protein Chem Struct Biol. 2015;100:1-31. doi: 10.1016/bs.apcsb.2015.06.002. Epub 2015 Jul 4.
PUPIL (Program for User Package Interfacing and Linking) implements a distinctive multi-scale approach to hybrid quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations. Originally developed to interface different external programs for multi-scale simulation with applications in the materials sciences, PUPIL is finding increasing use in the study of complex biological systems. Advanced MD techniques from the external packages can be applied readily to a hybrid QM/MM treatment in which the forces and energy for the QM region can be computed by any of the QM methods available in any of the other external packages. Here, we give a survey of PUPIL design philosophy, main features, and key implementation decisions, with an orientation to biomolecular simulation. We discuss recently implemented features which enable highly realistic simulations of complex biological systems which have more than one active site that must be treated concurrently. Examples are given.
PUPIL（用户包接口与链接程序）实现了一种独特的多尺度方法，用于混合量子力学/分子力学分子动力学（QM/MM-MD）模拟。PUPIL最初是为了连接不同的外部程序以进行多尺度模拟而开发的，应用于材料科学领域，如今在复杂生物系统的研究中得到了越来越广泛的应用。来自外部程序包的先进分子动力学技术可以很容易地应用于混合QM/MM处理，其中QM区域的力和能量可以通过任何其他外部程序包中可用的任何QM方法来计算。在这里，我们概述了PUPIL的设计理念、主要特性和关键实现决策，并以生物分子模拟为导向。我们讨论了最近实现的功能，这些功能能够对具有多个必须同时处理的活性位点的复杂生物系统进行高度逼真的模拟。文中给出了示例。
