Embedded Files
EasyHybrid is a graphical and interactive interface built on the pDynamo3 library, designed to enhance user experience and productivity. It is compatible with the ".pkl" serialization files generated by pDynamo, providing users with great flexibility. As a result, some tasks can be performed entirely within the graphical interface, while others—those requiring more customization—can be executed through traditional scripting, depending on the user's preference. Systems can be prepared within the interface and later loaded into scripts, and the results of simulations performed via scripts can be analyzed within the graphical environment.
Within the EasyHybrid graphical environment, users can interactively select atoms, define fixed regions, assign atoms to the quantum chemistry (QC) region (for purely quantum or hybrid simulations), edit systems, optimize geometries, and carry out various other routine procedures. This comprehensive toolset supports a wide range of molecular simulations, enabling researchers to conduct their work efficiently and effectively.
The interface has several types of representation, making visual inspections easier. Some examples can be seen in the figures below:
The MM and QC regions are represented by lines and balls and sticks. Fixed atoms are represented gray.
Cell and solvent box.
C-alpha trace
Van der Waals spheres
One of the advantages of the interface is that atoms that are to be fixed or assigned to a quantum region can be selected interactively. The figure below shows the same selection that is made in example9.py of the Hybrid Potentials tutorial, in which only one of the methyl groups of the blocked alanine molecule (bALA) is chosen to be in the quantum region.
Interactively selected atoms are represented by cyan dots.
The selection can be assigned to a quantum region by accessing the "Set As QC Atoms" option in the glArea selection menu, simply by right-clicking when there is an active selection.
EasyHybrid will represent the QC region in the form of balls and sticks. For clarity the configuration window indicating which QC method will be used has been omitted from the figures.
The implementation of a dynamic chemical bond representation and the plotting of interactive graphs were specially developed for analysis of trajectories involving chemical reactions.
If you are interested in this project and would like to collaborate, or simply use EasyHybrid, please visit the website: https://sites.google.com/view/easyhybrid/home?authuser=1
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