PES-trotter: A Cross-Platform Open-Source Application for the Analysis of Molecular Processes on 3D Potential-Energy Landscapes.

IF 2.9 3区化学 Q2 CHEMISTRY, MULTIDISCIPLINARY

Journal of Computational Chemistry Pub Date : 2026-05-30 DOI:10.1002/jcc.70397

Erwan Privat, Ajay Mohan Singh Rawat, Bernardo Ballotta, Antonino Polimeno, Sergio Rampino

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引用次数: 0

Abstract

We present PES-trotter, a cross-platform application for the exploration and analysis of 3D potential-energy landscapes generated from multi-dimensional potential-energy surfaces (PESs) of molecular systems. Inspired by the main ideas behind the previously released software AVATAR (Martino et al., Journal of Computational Chemistry 41 (2020): 1310-1323) relying on virtual-reality technology and third-party commercial software, PES-trotter is based on the open-source game engine Godot and related open-source assets, and introduces radically new important features for the navigation and topological analysis of the PES, among which the possibility of (1) navigating in walk, fly or free-mouse mode, (2) plotting energy profiles from custom curvilinear paths, (3) computing critical points and minimum-energy paths, and (4) playing back dynamical trajectories in first-person ride or spectator mode. Designed to match high portability and adaptability, PES-trotter can be run either as a stand-alone application on Windows, Linux, Android and macOS operating systems or in the window of a simple web browser on devices as widespread as mobile phones. In the article, the main features of PES-trotter are thoroughly described through two illustrative applications (the conformational analysis of a functionalized glycine and the analysis of classical trajectories for the H + LiH⁺ $\to$ H₂ + Li⁺ reactive process) highlighting the versatilty of PES-trotter as an innovative and accessible tool supporting chemical research and education.

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PES-trotter：一个跨平台的开源应用程序，用于分析三维势能景观的分子过程。

我们提出了PES-trotter，一个跨平台的应用程序，用于探索和分析由分子系统的多维势能面（PESs）产生的三维势能景观。受之前发布的软件AVATAR （Martino et al., Journal of Computational Chemistry 41(2020)）背后主要思想的启发：（1310-1323）基于虚拟现实技术和第三方商业软件，PES-trotter基于开源游戏引擎Godot和相关开源资产，为PES的导航和拓扑分析引入了全新的重要功能，其中(1)以步行，飞行或自由鼠标模式导航的可能性，(2)从自定义曲线路径绘制能量曲线，(3)计算关键点和最小能量路径，(3)计算关键点和最小能量路径。(4)以第一人称骑行或观众模式回放动态轨迹。PES-trotter的设计与高可移植性和适应性相匹配，既可以作为Windows、Linux、Android和macOS操作系统上的独立应用程序运行，也可以在手机等广泛使用的设备上的简单web浏览器窗口中运行。在本文中，PES-trotter的主要特点通过两个实例应用（功能化甘氨酸的构象分析和H+ LiH+→$$ \to $$ H2 + Li+反应过程的经典轨迹分析）进行了深入的描述，突出了PES-trotter作为支持化学研究和教育的创新和易于使用的工具的多功能性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Computational Chemistry 化学-化学综合

CiteScore

6.60

自引率

3.30%

发文量

247

审稿时长

1.7 months

期刊介绍： This distinguished journal publishes articles concerned with all aspects of computational chemistry: analytical, biological, inorganic, organic, physical, and materials. The Journal of Computational Chemistry presents original research, contemporary developments in theory and methodology, and state-of-the-art applications. Computational areas that are featured in the journal include ab initio and semiempirical quantum mechanics, density functional theory, molecular mechanics, molecular dynamics, statistical mechanics, cheminformatics, biomolecular structure prediction, molecular design, and bioinformatics.