GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
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DOI：
10.1002/jcc.24874
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发表时间：
2017-09-30
影响因子：
3
通讯作者：
Sugita, Yuji
中科院分区：
文献类型：
--
作者：
Kobayashi, Chigusa;Jung, Jaewoon;Sugita, Yuji
GENESIS （GENeralized-Ensemble SImulation System）是一个用于生物系统分子动力学（MD）模拟的软件包。通过采用高度并行化方案和增强的构象采样算法，扩展了系统大小和可访问时间尺度的限制。在这个新版本中，GENESIS 1.1增加了新的功能和先进的算法。除了CHARMM能量函数之外，AMBER和GROMACS包中使用的全原子和粗粒度势能函数现在也可用。通过进一步优化、多时间步长集成和混合（CPU+GPU）计算，MD仿真的性能得到了极大的提高。采用串法和具有灵活集体变量选择的复制交换伞取样法，寻找大分子构象变化的最小自由能途径，获得自由能谱。这些新功能增加了GENESIS在生物研究建模和仿真方面的实用性和能力。(c) 2017 Wiley期刊公司
GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU+GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. (c) 2017 Wiley Periodicals, Inc.