MD Simulation Services
At BioinformaticsDaily, we transform complex molecular interactions into actionable insights. Our state-of-the-art Molecular Dynamics (MD) Simulation services provide researchers, pharmaceutical companies, and biotech innovators with unparalleled molecular understanding.
Place Your Order
Submit your simulation request: Order Form
Why Choose Our MD Simulation Services
Advanced Software Infrastructure
- GROMACS 2024 - Industry-standard molecular simulation software
- High-performance computing infrastructure
- Secure data handling and storage
Comprehensive Analysis Suite
- Root Mean Square Deviation (RMSD)
- Root Mean Square Fluctuation (RMSF)
- Radius of Gyration (RG)
- Solvent Accessible Surface Area (SASA)
- Hydrogen Bond Analysis
- Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA)
- Principal Component Analysis (PCA) with Free Energy Landscape
Simulation Capabilities
- Protein-Protein Interactions
- Protein-Ligand Binding Studies
- Protein Structural Dynamics
- Custom simulation requirements available upon request
Deliverables
- Complete trajectory files
- Detailed analysis report
- Publication-ready figures
- Raw data for custom analysis
Pricing
| Protein Complex Size | Standard Processing | Parallel Processing* |
|---|---|---|
| < 600 Residues | 1,500 BDT ($13 USD) | 2,300 BDT ($21 USD) |
| < 1,000 Residues | 1,800 BDT ($16 USD) | 2,600 BDT ($24 USD) |
| > 1,000 Residues | Custom Quote | Custom Quote |
*Parallel Processing enables simultaneous simulation, reducing computation time (additional 800 BDT/$7 USD)
Place Your Order
Submit your simulation request: Order Form
Standard Simulation Package
- Production run: 100ns
- Analysis completion: Within 2 days of simulation completion
- Additional simulation time (200ns to 1000ns) available
- Custom timeline quotes for urgent projects
Technical Specifications
Simulation Parameters
- Force Field: Amber99sb-ildn
- Solvent Model: TIP3P Water
- System Configuration: Dodecahedron Unit Cell
- Equilibration: NVT and NPT for 1 ns each
- Simulation Temperature: 300 K
Advanced Algorithms
- LINCS for Covalent Bond Constraints
- Particle Mesh Ewald (PME) for Electrostatic Calculations
Supported Input Formats
- PDB files (preferred)
- Other molecular structure formats (.gro, .mol2, etc.)
- Custom structure files (please inquire)
Data Security
- Secure file transfer protocols
- Confidential data handling
- Data retention for 30 days post-delivery
- Extended storage options available
Service Timeline
- Order confirmation: Within 24 hours
- Custom quotes: Within 48 hours
- Standard simulations: 3-5 days
- Custom projects: Timeline provided with quote
Place Your Order
Submit your simulation request: Order Form
Contact Information
- Email: BioinformaticsDaily@gmail.com
- Response time: Within 24 hours
- Business hours: Monday-Friday, 9 AM - 6 PM (GMT+6)
- Emergency support available for ongoing simulations
Place Your Order
Submit your simulation request: Order Form
Accelerate Your Research with Confident Molecular Insights