GneimoSim: a modular internal coordinates molecular dynamics simulation package.
GneimoSim: a modular internal coordinates molecular dynamics simulation package.
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GneimoSim：模块化内坐标分子动力学模拟软件包。
DOI：
10.1002/jcc.23743
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发表时间：
2014
影响因子：
3
通讯作者：
Jain,Abhinandan
中科院分区：
文献类型：
--
作者：
Larsen,AdrienB;Wagner,JeffreyR;Kandel,Saugat;Salomon-Ferrer,Romelia;Vaidehi,Nagarajan;Jain,Abhinandan
广义牛顿-欧拉逆质量算符(GNEIMO)方法是求解内坐标分子动力学(ICMD)的一种先进方法。GNEIMO包括几个理论和算法方面的进步，以解决ICMD模拟方面的长期挑战。在本文中，我们描述了实现GNEIMO方法的GneimoSim ICMD软件包。我们相信，GneimoSim是第一个包括高级功能的软件包，例如内部坐标的均分原理，以及一种包括Fixman势的方法，以消除使用硬约束带来的系统统计偏差。此外，通过设计，GneimoSim是可扩展的，并且可以很容易地与用于ICMD模拟的第三方力场包接口。目前，GneimoSim包括与LAMMPS、OpenMM和Rosetta力场计算程序包的接口。底层C++类及其方法提供了全面的Python接口，这为用户开发模拟脚本以配置模拟和控制模拟流程提供了强大而通用的机制。GneimoSim已被广泛用于研究蛋白质结构的动力学，改进蛋白质同源模型，并通过改进的采样方法模拟大规模的蛋白质构象变化。GneimoSim不仅限于蛋白质，还可以用于模拟聚合物材料。
The generalized Newton–Euler inverse mass operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this article, we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, and Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials.