MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations

Area of Science:

• Computational Chemistry
• Biophysics
• Molecular Modeling

Background:

• Molecular dynamics (MD) simulations are crucial for understanding molecular behavior.
• Preparing input files for MD simulations requires significant user expertise.
• Existing methods present a steep learning curve for novice researchers.

Purpose of the Study:

• To introduce MDBuilder, a user-friendly PyMOL plugin for preparing MD simulation systems.
• To simplify the creation of starting structures for multiple popular MD simulation packages.
• To lower the barrier to entry for researchers new to MD simulations.

Main Methods:

• Developed MDBuilder as a platform-independent PyMOL plugin using Python.
• Implemented a menu-oriented, point-and-click graphical user interface (GUI).
• Tested the plugin on Windows and Linux operating systems.

Main Results:

• MDBuilder successfully assists in building starting structures for MD simulations.
• The GUI facilitates easier preparation of input files for CHARMM force field-based simulations.
• The tool is accessible to both beginners and experienced users.

Conclusions:

• MDBuilder significantly enhances the usability of molecular dynamics simulations.
• The plugin democratizes access to advanced computational chemistry techniques.
• MDBuilder is freely available, promoting wider adoption and research.