Molecular Dynamics Pipeline
High-performance simulations to understand biomolecular motion, interactions, and function
Understanding Molecular Dynamics
Molecular dynamics (MD) simulations provide atomic-level insights into the motion and interactions of biological macromolecules. Our pipeline integrates state-of-the-art algorithms with high-performance computing to deliver accurate and efficient simulations.
From system preparation to trajectory analysis, our platform streamlines the entire MD workflow, making advanced simulations accessible to researchers across disciplines.
High-Performance Computing
Leverage GPU acceleration and distributed computing for faster simulations
Multiple Force Fields
Choose from a variety of force fields for different biomolecular systems
Comprehensive Analysis
Extract meaningful insights with our suite of analysis tools
Key Features
Our molecular dynamics pipeline offers a comprehensive suite of tools for simulation and analysis
- 1Multiple integrators for different simulation types
- 2Support for various thermostats and barostats
- 3Enhanced sampling techniques (umbrella sampling, metadynamics)
- 4GPU-accelerated calculations for faster results
- 1Automated topology generation and parameterization
- 2Intelligent solvent box creation and ion placement
- 3Support for membrane proteins and lipid bilayers
- 4Custom ligand parameterization and integration
- 1RMSD, RMSF, and radius of gyration calculations
- 2Hydrogen bond and contact analysis
- 3Principal component analysis and essential dynamics
- 4Free energy calculations and binding affinity estimation
Our Workflow
From system preparation to analysis, our platform guides you through every step of the molecular dynamics process
Structure Preparation
Start with a protein structure from our structure prediction pipeline or upload your own. Our system automatically checks for missing residues, adds hydrogens, and prepares the structure for simulation.
System Setup
Define your simulation environment with our intuitive interface. Choose force fields, add solvent, ions, ligands, or membrane components as needed for your system.
# Example system configuration
forcefield: AMBER99SB-ILDN
water_model: TIP3P
box_type: dodecahedron
box_distance: 1.0 nm
neutralize: true
ion_concentration: 0.15 M NaClSimulation Protocol
Configure your simulation protocol with our template-based system. Choose from standard protocols or customize every aspect of your simulation, from energy minimization to production runs.
Simulation Execution
Run your simulation on our high-performance computing infrastructure. Monitor progress in real-time, with automatic checkpointing and the ability to extend simulations as needed.
Analysis & Visualization
Analyze your simulation results with our comprehensive suite of tools. Generate publication-quality figures, extract meaningful metrics, and gain insights into your molecular system.
Applications & Use Cases
Our molecular dynamics pipeline supports a wide range of research and development applications
Ligand Binding & Drug Discovery
Understand the dynamics of protein-ligand interactions to accelerate drug discovery. Calculate binding free energies, identify key interactions, and optimize lead compounds.
- Binding free energy calculations (MM/PBSA, MM/GBSA)
- Residence time estimation for drug candidates
- Binding pathway elucidation with enhanced sampling
- Structure-activity relationship insights
Technical Specifications
Our platform integrates cutting-edge technologies for high-performance molecular dynamics simulations
GROMACS Integration
High-performance MD engine with GPU acceleration
AMBER Support
Industry-standard force fields and simulation protocols
OpenMM Framework
Flexible and extensible simulation toolkit
Custom Integrations
Support for specialized simulation packages
GPU Acceleration
NVIDIA and AMD GPU support for faster calculations
Cloud Integration
Seamless scaling to cloud resources as needed
Job Scheduling
Intelligent resource allocation and queue management
Checkpoint & Restart
Robust handling of long simulations with automatic recovery
Ready to Run Molecular Dynamics?
Join our platform today and access cutting-edge tools for molecular dynamics simulations and analysis.