Visual Dynamics

Visual Dynamics automates the setup, execution, and analysis of molecular dynamics simulations using GROMACS to evaluate protein and protein–ligand systems.

Key Features:

• Simulation engine: Uses GROMACS as the underlying molecular dynamics engine.
• Automation: Automates generation and execution of molecular simulations.
• Supported system types: Supports protein-only systems and protein–ligand complexes.
• Ligand preparation: Supports ligand topology and parameter generation via ACPYPE or PRODRG.
• Input handling: Accepts protein inputs in apo form or complexed with ligands.
• Outputs: Produces downloadable graphical analyses and log files reporting kinetic and thermodynamic characteristics.

Scientific Applications:

• Biomolecular dynamics: Investigate dynamic behavior of proteins and protein–ligand complexes.
• Kinetic and thermodynamic analysis: Derive kinetic and thermodynamic characteristics from simulation outputs.
• Bioinformatics workflows: Integrate automated MD simulations into computational biology research pipelines.

Methodology:

Automates simulation preparation and execution using GROMACS, supports ligand topology generation with ACPYPE or PRODRG, and generates graphical analysis and log files.