EasyHybrid

EasyHybrid is a free and open-source graphical environment for molecular system simulations built upon the pDynamo3 simulation library. It provides access to most of pDynamo’s core functionalities through an intuitive interface, allowing users to import, edit, and inspect pDynamo systems. Additionally, it supports the import and export of systems using standard file formats or pDynamo serialization files. This integration enables users to combine the convenience of visual inspection and editing with the flexibility of Python 3 scripting for executing pDynamo-based simulations.

The interface was primarily designed to facilitate the determination of reaction pathways in biological systems using hybrid quantum chemical/molecular mechanical (QC/MM) methods. Nevertheless, EasyHybrid also provides access to the full range of pDynamo functionalities through its graphical environment, including:

• Import systems in various formats and force fields compatible with pDynamo3.

• Viewing, inspecting, editing and exporting pDynamo3 serialization files.

• Pure quantum chemistry (QC) simulations, both ab initio and semi-empirical

• Pure molecular mechanics (MM) simulations using AMBER, CHARMM, or OPLS force fields

• Hybrid QC/MM simulations

• Single point calculations

• Energy minimization

• Molecular dynamics

• Normal modes

• Reaction coordinate scanning

• Umbrella sampling

• Reaction path calculations

EasyHybrid emerged as an evolution of its predecessor, GTKDynamo—a graphical interface that integrated pDynamo with the widely used PyMOL biomolecular viewer. The decision to discontinue the use of PyMOL as the visualization backend stemmed from its progressive shift toward proprietary software characteristics, as well as the lack of control over its version updates. In response to this limitation, a new project was initiated to develop a custom API based on modern OpenGL. This API now underpins the graphical (GL) component of EasyHybrid and can be readily adapted for use in other GTK-based projects requiring three-dimensional visualization of molecular systems.

Contact:  easyhybrid3@gmail.com