GeomBD3

GeomBD3 simulates Brownian dynamics of all-atom rigid molecular models using overdamped Langevin dynamics to compute molecular association rates and characterize recognition processes.

Key Features:

• All-atom rigid models: simulates rigid molecular structures at all-atom resolution undergoing diffusion.
• Overdamped Langevin dynamics: governs molecular diffusion using an overdamped Langevin framework.
• Interaction potentials: models electrostatic forces, Lennard-Jones potentials, and ligand desolvation interactions.
• Automated kinetics metrics: computes molecular association rates, surface residence times, and association statistics based on user-defined criteria.
• Post-processing analyses: extracts molecular association pathways, diffusion coefficients, intermolecular interaction energies, and intermolecular contact probability maps via supplementary analysis scripts.
• Configurable environments: supports simulations across diverse environments and configurations.

Scientific Applications:

• Protein–ligand interactions: quantifies association rates and pathways for protein–ligand systems.
• Nucleic acid biosensors: studies dynamics and recognition in large nucleic acid biosensor constructs.
• Small-molecule and macromolecular systems: applies to both small molecule and large biomolecular assemblies.
• Rational design and interpretation: supports rational design of engineered systems and provides explanatory insights complementary to experimental data.

Methodology:

Simulates diffusion of all-atom rigid molecules via overdamped Langevin dynamics with electrostatic, Lennard-Jones, and ligand desolvation interactions, performs automated calculations of association rates, surface residence times, and association statistics, and uses bundled analysis scripts to extract association pathways, diffusion coefficients, interaction energies, and contact probability maps.