LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems

Area of Science:

• Computational chemistry
• Molecular dynamics simulations
• Structural biology

Background:

• Molecular simulations are crucial for understanding biomolecular systems.
• Ring penetrations, caused by artifacts like long bonds, can compromise simulation accuracy.
• Existing methods for artifact correction often require significant user intervention.

Purpose of the Study:

• To develop an automated workflow for correcting ring penetrations in molecular simulations.
• To provide a user-friendly tool that minimizes manual input for artifact resolution.
• To enhance the reliability of classical molecular dynamics (MD) simulations.

Main Methods:

• Implementation of a VMD plugin named LongBondEliminator.
• Detection of ring piercing artifacts via identification of long, strained bonds.
• Automated treatment of problematic regions using multiple biases in NAMD (NAMD).
• Combination of collective variables, density-based forces, and alchemical techniques within NAMD.

Main Results:

• Successfully demonstrated the elimination of ring penetrations in three complex systems: a lignin polymer, a viral capsid, and the protein aggrecan.
• The LongBondEliminator tool effectively alleviates long bonds, a common artifact in simulation systems.
• The workflow requires minimal user input for artifact correction.

Conclusions:

• LongBondEliminator offers a robust and automated solution for correcting ring penetrations in MD simulations.
• The tool is versatile and applicable to a wide range of biomolecular simulation systems.
• This method enhances the quality and reliability of structural data obtained from molecular simulations.