Molecular dynamics simulation with full trajectory analysis
Take a docked complex and test whether it stays stable in water. ReactorMD builds the system, runs GROMACS minimisation, NVT and NPT equilibration and a production simulation, then delivers the trajectory with a complete analysis.
Who this service is for
- Students and researchers who need MD to support a docking study
- Groups without GPU time or GROMACS experience
- Anyone who wants a documented, reproducible simulation setup
What to send us
- A protein–ligand complex (for example a docked pose) or an apo protein
- Preferred force field if you have one; otherwise a standard choice is used
- Simulation length (25, 50, 100, 200 or 500 ns)
- Whether the system is soluble or membrane-embedded
How the work is done
- Prepare the protein topology and check chains, termini and missing atoms.
- Parametrise the ligand and merge it into the system topology.
- Build the periodic box, solvate and add ions to neutralise and reach physiological salt.
- Minimise the energy to remove bad contacts.
- Equilibrate in NVT and then NPT with restraints so the system relaxes without drifting.
- Run the production simulation and process the trajectory.
- Analyse and report RMSD, RMSF, radius of gyration, SASA, hydrogen bonds, PCA and free-energy landscapes.
What you receive
- Production trajectory and final structures
- RMSD, RMSF, Rg, SASA and hydrogen-bond plots
- PCA and free-energy landscape figures
- Equilibration quality plots (temperature, pressure, density, energy)
- Methods report and a ZIP with inputs, parameters and results
Simulation packages & turnaround
| Simulation Length | Apo Protein MD (USD) | Protein–Ligand Complex MD (USD) | Estimated Turnaround |
|---|---|---|---|
| 25 ns | $8.00 | $15.00 | Up to 8–12 hours |
| 50 ns | $15.00 | $25.00 | Up to 12–18 hours |
| 100 ns | $30.00 | $49.90 | Up to 24–36 hours |
| 200 ns | $55.00 | $99.00 | Up to 48–60 hours |
| 500 ns | $125.00 | $199.00 | Up to 72–96 hours |
What this method can and cannot tell you
MD samples motion over a limited time. A 25 to 100 ns run shows stability and local flexibility but cannot prove binding or capture slow events. Results depend on the force field and starting structure, and should be read together with other evidence.
Frequently asked questions
How long should a protein–ligand MD simulation be?
Many studies use 50 to 100 ns to assess complex stability. Shorter runs are fine for screening-level checks, while flexible systems and free-energy work may need several hundred nanoseconds.
Which software runs the simulations?
ReactorMD uses GROMACS, a widely used open-source MD engine, with documented force fields and settings.
Is trajectory analysis included in the price?
Yes. The MD workflow includes the standard analysis suite and figures, so you do not pay separately for RMSD, RMSF, Rg, SASA, hydrogen bonds, PCA and free-energy landscapes.
Can you simulate membrane proteins such as GPCRs?
Yes. Membrane systems need extra setup (lipid bilayer building and longer equilibration). Tell us the protein and requirements when you start the project.
What do I receive when the simulation finishes?
A ZIP with the trajectory, analysis figures and data files, equilibration plots, input and parameter files and a methods report.
Related services
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Learn more
Build topologies, solvate and neutralise, minimise, equilibrate in NVT then NPT, run production, then correct periodic boundaries before analysis.
MD analysis guideHow to Interpret MD Simulation Results: RMSD, RMSF, Rg, SASALook for convergence, not single numbers. Combine several metrics before concluding that a ligand is stably bound.
Ready to start?
Tell us about your target and compounds. The price and scope are confirmed before payment.
Computational results are predictions and support, but do not replace, experimental validation. Page reviewed by ReactorMD, 16 October 2026.