标题： PLUMED-GUI：用于分子动力学分析和偏置脚本交互式开发的环境 显示英文标题

标题： PLUMED-GUI: an environment for the interactive development of molecular dynamics analysis and biasing scripts

摘要： PLUMED-GUI 是一个交互式环境，可在 Visual Molecular Dynamics (VMD) 环境中开发和测试复杂的 PLUMED 脚本。 计算生物物理学家可以利用 PLUMED 的丰富语法来定义集体变量（CVs），同时利用 VMD 的化学感知原子选择语言，在自然的点击界面中进行操作。 预定义的模板和语法记忆有助于定义已知的反应坐标。 复杂的 CVs，例如涉及用于 RMSD 或天然接触计算的参考快照，可以通过提供可用选项概览的对话框构建。 脚本可以导出用于模拟程序，或在当前加载的分子轨迹上进行评估。 脚本的开发无需离开 VMD，从而为分子度量提供了逐步尝试-查看-修改的开发模式。 显示英文摘要

摘要： PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective variables (CVs) and VMD's chemically-aware atom selection language, while working within a natural point-and-click interface. Pre-defined templates and syntax mnemonics facilitate the definition of well-known reaction coordinates. Complex CVs, e.g. involving reference snapshots used for RMSD or native contacts calculations, can be built through dialogs that provide a synoptic view of the available options. Scripts can be either exported for use in simulation programs, or evaluated on the currently loaded molecular trajectories. Development of scripts takes place without leaving VMD, thus enabling an incremental try-see-modify development model for molecular metrics.