Calculation of 1D and 2D densities in VMD: A flexible and easy-to-use code

Characterization of structural information at the atomistic level in molecular dynamics (MD) simulations is a necessary task for researchers in the fields of materials modeling and simulation. Visualization of the density distribution is typically one of the most important properties in structural characterization. Visual Molecular Dynamics (VMD) is a widely used molecular visualization package that can not only visualize complex molecular systems but also perform analysis by integrating special plugins or by running in-house generated TCL scripts. However, a density analysis is still not an in-built feature of VMD. This work presents a flexible and easy-to-use TCL code to be used in VMD, that can perform both 1D and 2D density calculations over any specified local areas of a given system. By using the built-in commands of VMD, the code can access and process trajectory files in any formats that are supported by VMD, as produced by mainstream simulation packages, i.e., LAMMPS, GROMACS, NAMD, and CHARMM, etc. This work introduces the calculation method, code, and usages in detail to provide a quick start for users in their density analysis work.

在分子动力学（MD）模拟中对原子级别结构信息的表征，对于材料建模与模拟领域的研究人员而言是一项不可或缺的任务。密度分布的可视化通常被视为结构表征中最为重要的属性之一。可视化分子动力学（VMD）是一款广泛应用的分子可视化软件包，它不仅能够可视化复杂的分子系统，还能够通过集成特定的插件或运行内部生成的TCL脚本来进行分析。然而，密度分析并非VMD的内置功能。本研究提出了一种灵活且易于使用的TCL代码，可在VMD中执行，能够对指定系统中的任何局部区域进行一维和二维密度计算。通过利用VMD的内置命令，该代码能够访问并处理VMD支持的所有格式轨迹文件，即由主流模拟软件包（如LAMMPS、GROMACS、NAMD和CHARMM等）生成的轨迹文件。本研究详细介绍了计算方法、代码及其用法，以便为用户在密度分析工作中的快速入门提供指导。