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.

Program summary

Program title: DensityCalculator

CPC Library link to program files: https://doi.org/10.17632/vcbh2gt8wg.1

Developer's repository link: https://github.com/yuxiangwang321/DensityCalculator

Licensing provisions: GPLv3

Programming language: TCL/TK

External routines: VMD (version 1.9.3, http://www.ks.uiuc.edu/Research/vmd/)

Nature of problem: Calculate mass or number density distribution from trajectory files in VMD, and project the density along a specified 1D axis or onto a specified 2D plane.

Solution method: The 1D or 2D density distribution is calculated through the following steps: slice the concerned area with specified resolutions in X, Y, and Z directions; then the mass or atom number in each unit slice (or cuboid in 2D case) is calculated; if there are multiple frames, average the mass or atom number by the frame number; finally, density in each unit is divided by the slice volume to get the density.

Additional comments including restrictions and unusual features: The code must be run with VMD as a platform, the current version only can only calculate mass or number density.

The code can calculate both 1D and 2D density distributions in any specified local or global areas of the system.

中文翻译：

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VMD中一维和二维密度的计算：灵活易用的代码

在分子动力学（MD）模拟中，原子级的结构信息表征是材料建模和模拟领域研究人员的一项必要任务。密度分布的可视化通常是结构表征中最重要的属性之一。Visual Molecular Dynamics（VMD）是一种广泛使用的分子可视化程序包，它不仅可以可视化复杂的分子系统，还可以通过集成特殊插件或运行内部生成的TCL脚本来执行分析。但是，密度分析仍不是VMD的内置功能。这项工作提出了一种可在VMD中使用的灵活且易于使用的TCL代码，该代码可以在给定系统的任何指定局部区域上执行1D和2D密度计算。通过使用VMD的内置命令，

计划摘要

程序标题： DensityCalculator

CPC库链接到程序文件： https : //doi.org/10.17632/vcbh2gt8wg.1

开发人员的资料库链接： https : //github.com/yuxiangwang321/DensityCalculator

许可条款： GPLv3

编程语言： TCL / TK

外部例程： VMD（1.9.3版，http ： //www.ks.uiuc.edu/Research/vmd/）

问题性质：根据VMD中的轨迹文件计算质量或数量密度分布，然后沿指定的1D轴或指定的2D平面投影密度。

求解方法：通过以下步骤计算一维或二维密度分布：在X，Y和Z方向上以指定的分辨率对相关区域进行切片；然后计算每个单位切片中的质量或原子数（在二维情况下为长方体）；如果有多个框架，则通过框架编号对质量数或原子数求平均值；最后，将每个单位的密度除以切片体积即可得出密度。

其他注释包括限制和异常功能：该代码必须以VMD为平台运行，当前版本只能计算质量​​或数量密度。

该代码可以计算系统的任何指定局部或全局区域中的1D和2D密度分布。