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

Area of Science:

• Computational Chemistry
• Biomolecular Simulations
• Software Development

Background:

• Hybrid quantum chemical/molecular mechanical (QC/MM) simulations are crucial for studying complex chemical processes in biological systems.
• Existing software often lacks user-friendly interfaces for preparing and executing these advanced simulations.

Purpose of the Study:

• To introduce EasyHybrid, a novel graphical user interface (GUI) for simplifying hybrid QC/MM simulations.
• To provide an integrated platform for simulation setup, execution, and analysis.

Main Methods:

• Development of a free and open-source GUI built upon the pDynamo3 library.
• Implementation of features for system preparation, inspection, and editing.
• Support for diverse simulation types including molecular dynamics, Nudged Elastic Band, and umbrella sampling.

Main Results:

• EasyHybrid offers an intuitive environment for managing molecular systems and simulation workflows.
• Advanced 3D visualization, interactive editing, and flexible atom selection enhance usability.
• Automated log parsing and trajectory analysis streamline data interpretation.

Conclusions:

• EasyHybrid provides a powerful, user-friendly solution for researchers performing quantum chemistry and hybrid QC/MM simulations.
• The software facilitates efficient setup and analysis, making advanced computational techniques more accessible.