Molecular Dynamics Simulation Services
Service Features
We provide professional molecular dynamics simulation services, supporting end-to-end delivery from model construction and parameter optimization to result analysis and visualization. Leveraging our in-house high-performance computing cluster, we ensure massive computational power and rapid parallel processing. A strict confidentiality agreement is also signed to fully protect your research outcomes and data security.
Service Introduction
We simulate the dynamic behavior of biological macromolecules under physiological conditions at the atomic scale, revealing their stability, flexibility, and conformational changes.
Service Advantages
- Realistic Environmental Simulation: Water, ions, temperature, and pressure.
- Dynamic Process Tracking: RMSD, RMSF, PCA, and FEL analyses.
- Visualized Animations: Intuitive display of molecular motion.
Service Process
Customer Requirements
Initial Structure (docking results or experimental structure)
Simulation Time Requirements (in nanoseconds, ns)
Regions of Interest (e.g., active site, loop regions)
Service Description
| Service Name |
Service Description |
Deliverables & Specifications |
Turnaround (Business Days) |
| Molecular Dynamics Simulation |
System setup (solvent, ions, force field), energy minimization & equilibration, production simulation, trajectory analysis, and animation generation. |
Deliverables: |
3-5 |
|
• Equilibrated initial structure file |
|||
|
• System setup parameters and log files |
|||
|
• RMSD vs. time plot |
|||
| • RMSF vs. residue index plot | |||
| • Structure flexibility coloring (blue = low flexibility, red = high flexibility) | |||
| • Radius of gyration (Rg) plot | |||
| • 2D/3D scatter plots projected onto principal components | |||
| • Free energy landscape (FEL) plot | |||
| • High-resolution simulation trajectory video (MP4/AVI format) | |||
| Specifications: | |||
| • Simulation duration: 50–100 ns (adjustable based on system) | |||
| • Assurance of system equilibration | |||
| • Complete trajectory analysis and visualization results provided |
Case Studies
Ready to Start Your Project?
Our expert team is ready to support your computational biology research. Get in touch with us for a consultation or request a quote today.
Contact Our ExpertsQ&A
How long should the simulation be?