• EasyHybrid: An Interactive Gra...

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

Title:
EasyHybrid: An Interactive Graphical Environment for Quantum, Classical and Hybrid Simulations with pDynamo3.
Authors:
Bachega JFR; Department of Pharmacosciences, Federal University of Health Sciences of Porto Alegre, 90050-170 Porto Alegre, RS, Brazil.; Biotechnology Center, Graduate Program in Molecular and Cellular Biology, Federal University of Rio Grande do Sul, 90650-001 Porto Alegre, RS, Brazil., Hagen G; Biotechnology Center, Graduate Program in Molecular and Cellular Biology, Federal University of Rio Grande do Sul, 90650-001 Porto Alegre, RS, Brazil., Sequeiros-Borja C; Tunneling Group, Biotechnology Center, Krzywoustego 8, 44-100 Gliwice, Poland., Nikklas K; 3D Development, deCode GmbH, 46145 Oberhausen, Germany., Chahine J; Biological Structures Group, Multiuser Center for Biomolecular Innovation, São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil., Timmers LFMS; Graduate Program in Biotechnology, University of Vale do Taquari, 95900-000 Lajeado, RS, Brazil., Field MJ; Laboratoire de Chimie et Biologie des Métaux, UMR5249, Université Grenoble I, CEA, CNRS, 38054 Grenoble, France.; Theory Group, Institut Laue-Langevin, 38042 Grenoble, France.
Source:
Journal of chemical information and modeling [J Chem Inf Model] 2026 Feb 09; Vol. 66 (3), pp. 1286-1292. Date of Electronic Publication: 2025 Nov 11.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-960X (Electronic) Linking ISSN: 15499596 NLM ISO Abbreviation: J Chem Inf Model Subsets: MEDLINE
Imprint Name(s):
Original Publication: Washington, D.C. : American Chemical Society, c2005-
MeSH Terms:
Quantum Theory* , Molecular Dynamics Simulation* , Software* , Computer Graphics*, User-Computer Interface
References:
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Entry Date(s):
Date Created: 20251111 Date Completed: 20260209 Latest Revision: 20260213
Update Code:
20260213
PubMed Central ID:
PMC12892311
DOI:
10.1021/acs.jcim.5c02047
PMID:
41218170
Database:
MEDLINE

*Further Information*

*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.*