标题： METAGUI 3：用于在分子动力学模拟中选择集体变量的图形用户界面 显示英文标题

标题： METAGUI 3: a graphical user interface for choosing the collective variables in molecular dynamics simulations

摘要： 分子动力学（MD）模拟通过积分其组成原子的运动方程，允许探索生物聚合物的相空间。 MD轨迹的分析通常依赖于选择沿其投影系统动力学的集体变量（CVs）。 我们开发了一个图形用户界面（GUI），以促进适当CVs的交互式选择。 GUI允许：交互式地定义新的CVs；将配置划分为由CVs相似值表征的微状态；计算无偏和有偏（元动力学）模拟的微状态自由能；将微状态聚类到动能盆地中；将自由能景观可视化为用于分析的CVs子集的函数。 简单的鼠标点击即可快速检查景观中特定点对应的结构。 显示英文摘要

摘要： 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.