METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations
METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations
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DOI：
10.1016/j.cpc.2017.04.009
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发表时间：
2017-08-01
影响因子：
6.3
通讯作者：
Rodriguez, Alex
中科院分区：
文献类型：
--
作者：
Giorgino, Toni;Laio, Alessandro;Rodriguez, Alex
分子动力学（MD）模拟允许通过整合其组成原子的运动方程来探索生物聚合物的相空间。MD轨迹的分析通常依赖于集体变量（CV）的选择，系统的动态特性沿着集体变量（CV）沿着被投影。我们开发了一个图形用户界面（GUI），以促进适当的CV的交互式选择。GUI允许：交互定义新CV;将配置划分为以CV的相似值为特征的微观状态;计算无偏和有偏（元自相关）模拟的微观状态的自由能;在动力学盆地中聚类微观状态;将自由能景观可视化为用于分析的CV的子集的函数。一个简单的鼠标点击允许一个快速检查结构对应于特定点的景观。程序摘要程序标题：METAGUI 3程序文件doi：http://dx.doi.org/10.17632/wyxjndwkbp.1Licensing规定：GPL v3编程语言：Tcl/Tk，Fortran以前版本的期刊参考：METAGUI [1]新版本是否取代以前的版本？：问题性质：选择合适的集合变量，通过有偏和无偏的分子动力学来描述生物分子系统的热力学和动力学。解决方法：提供一个环境来计算和可视化自由能表面作为集合变量的函数，交互定义。附加注释：METAGUI 3不是一个独立的程序，而是一个插件，提供VMD（版本1.9.2或更高版本）中的分析功能。[1]X. Biarnes，F. Pietrucci，F. Marinelli，A.莱奥，梅塔圭。用于分析元动力学和分子动力学模拟的VMD接口，计算机物理通讯183（2012）203-211。(C)2017由Elsevier B. V.出版
Molecular dynamics (MD) simulations allow the exploration of the phase space of biopolymers through the integration of equations of motion of their constituent atoms. The analysis of MD trajectories often relies on the choice of collective variables (CVs) along which the dynamics of the system is projected. We developed a graphical user interface (GUI) for facilitating the interactive choice of the appropriate CVs. The GUI allows: defining interactively new CVs; partitioning the configurations into microstates characterized by similar values of the CVs; calculating the free energies of the microstates for both unbiased and biased (metadynamics) simulations; clustering the microstates in kinetic basins; visualizing the free energy landscape as a function of a subset of the CVs used for the analysis. A simple mouse click allows one to quickly inspect structures corresponding to specific points in the landscape.Program summaryProgram Title: METAGUI 3Program Files doi: http://dx.doi.org/10.17632/wyxjndwkbp.1Licensing provisions: GPLv3Programming language: Tcl/Tk, FortranJournal reference of previous version: METAGUI [1]Does the new version supersede the previous version?: NoNature of problem: Choose the appropriate collective variables for describing the thermodynamics and kinetics of a biomolecular system through biased and unbiased molecular dynamics.Solution method: Provide an environment to compute and visualize free energy surfaces as a function of collective variables, interactively defined.Additional comments: METAGUI 3 is not a standalone program but a plugin that provides analysis features within VMD (version 1.9.2 or higher).[1] X. Biarnes, F. Pietrucci, F. Marinelli, A. Laio, METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations, Computer Physics Communications 183 (2012) 203-211. (C) 2017 Published by Elsevier B.V.