EasyHybrid: An Interactive Graphical Environment for Quantum, Classical and Hybrid Simulations with pDynamo3

We present EasyHybrid, a free and open-source graphical interface for hybrid quantum chemical/molecular mechanical (QC/MM) simulations built on the pDynamo3 library. The software provides an intuitive environment for preparing, inspecting, and editing molecular systems, while supporting a broad range of simulations, including reaction coordinate scans, molecular dynamics, normal-mode analysis, Nudged Elastic Band, and umbrella sampling. Key features include advanced 3D visualization of large biomolecular systems, interactive editing, flexible atom selection, system pruning for efficient QC/MM setup, orbital and electrostatic potential surfaces, automated log parsing, and trajectory analysis. EasyHybrid integrates these tools into a single platform, offering a familiar yet specialized environment for quantum chemistry and hybrid QC/MM simulations.

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Publication Details

Journal
Journal of Chemical Information and Modeling
Published
2025-11-11
DOI
https://doi.org/10.1021/acs.jcim.5c02047
Primary Topic
Machine Learning in Materials Science
Type
article
Field-Weighted Citation Impact
0.00
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article

EasyHybrid: An Interactive Graphical Environment for Quantum, Classical and Hybrid Simulations with pDynamo3

Luís Fernando Saraiva Macedo Timmers, G. Hagen, José Fernando Ruguiero Bachega, Jorge Chahine et al.
Journal of Chemical Information and Modeling
Machine Learning in Materials Science
article

EasyHybrid: An Interactive Graphical Environment for Quantum, Classical and Hybrid Simulations with pDynamo3

Luís Fernando Saraiva Macedo Timmers, G. Hagen, José Fernando Ruguiero Bachega, Jorge Chahine, Martin J. Field, Carlos Eduardo Sequeiros-Borja, Kai Nikklas
article en

Abstract

We present EasyHybrid, a free and open-source graphical interface for hybrid quantum chemical/molecular mechanical (QC/MM) simulations built on the pDynamo3 library. The software provides an intuitive environment for preparing, inspecting, and editing molecular systems, while supporting a broad range of simulations, including reaction coordinate scans, molecular dynamics, normal-mode analysis, Nudged Elastic Band, and umbrella sampling. Key features include advanced 3D visualization of large biomolecular systems, interactive editing, flexible atom selection, system pruning for efficient QC/MM setup, orbital and electrostatic potential surfaces, automated log parsing, and trajectory analysis. EasyHybrid integrates these tools into a single platform, offering a familiar yet specialized environment for quantum chemistry and hybrid QC/MM simulations.

Journal of Chemical Information and ModelingVol. 66(3)
Univates (BR), Centre National de la Recherche Scientifique (FR), Universidade Federal do Rio Grande do Sul (BR), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR), CEA Grenoble (FR), Evangelisches Krankenhaus Oberhausen (DE), Institut Laue-Langevin (FR), Immunosciences Lab (United States) (US), Laboratoire de Chimie et Biologie des Métaux (FR), Cellular Therapeutics (United Kingdom) (GB), Łukasiewicz Research Network - Institute of Welding (PL), Institut de Biologie Moléculaire et Cellulaire (FR), University of Health Sciences (SO), Fresenius Kabi (Czechia) (CZ), University of Health Sciences Antigua (AG), Universidade Estadual Paulista (Unesp) (BR), Université Grenoble Alpes (FR), University of Rio Grande and Rio Grande Community College (US)
Openalex Percentile: Top 73%
Machine Learning in Materials Science
DOIOpen Access PDFOpenAlex
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