EasyHybrid
EashyHybrid is a graphical environment for molecular system simulations based on the pDynamo3 simulation library. It allows users to access most of pDynamo's basic functionality via its interface, to construct, edit and inspect pDynamo systems, and import and export them using standard file formats or pDynamo serialization files. This enables users to combine the convenience of inspection and editing within the graphical environment while leveraging the flexibility of Python3 to execute pDynamo scripts.
The interface was designed primarily to make it easy to determine reaction pathways in biological systems using hybrid quantum chemical/molecular mechanical (QC/MM) methods. However, EasyHybrid allows users to access the full range of pDynamo capabilities via 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 the project that preceded it, called GTKDynamo, a graphical interface that integrated pDynamo with the famous PyMOL biomolecular viewer. The decision to no longer use PyMOL as a basis for visualization was due to the fact that it is increasingly acquiring characteristics of proprietary software, and we also lack control over version updates. This situation gave rise to another project where we implemented our own API in modern OpenGL. This API is used as a basis for the GL area of EasyHybrid and can also be easily applied to other projects in GTK that require the three-dimensional visualization of molecular systems.
Contact:Â easyhybrid3@gmail.com