ChemServerOnline molecular dynamics simulation
Take a docked complex into explicit water and watch whether the ligand stays. ChemServer sets up, runs and analyses protein ligand MD on GPU servers, from the force field to the final plots.
Available on request. Molecular dynamics runs on dedicated GPU servers and is opened per account. Email chris@chemserver.online with your system (protein, ligand, number of atoms if you know it) and the simulation length you need.
Why run MD after docking
Docking gives a single frozen pose and an approximate score. A molecular dynamics simulation lets the protein, the ligand and the water move for nanoseconds to hundreds of nanoseconds. A pose that drifts away or loses its key hydrogen bonds was probably not right; a pose that stays put is far more convincing in a paper or a project report.
Set up
| Step | Options |
|---|---|
| Complex | Upload a protein ligand PDB, pick a docked pose from My Files, or give protein and ligand separately |
| Ligand | Residue, net charge, AM1-BCC or Gasteiger charges, SMILES for bond orders |
| Protein | Protonation pH, chains, missing atoms and residues, chain end caps |
| Force field | AMBER ff14SB, AMBER ff19SB, CHARMM36m, OPLS-AA/M; ligands with GAFF2, OpenFF Sage, CGenFF or Espaloma |
| Water and ions | TIP3P, OPC, TIP4P-Ew or SPC/E; rectangular, cubic, truncated octahedron or rhombic dodecahedron box; neutralizing ions and NaCl or KCl |
Simulation protocol
- Energy minimization, NVT and NPT equilibration with heavy atom restraints.
- Production runs from 1 to 500 ns, with up to 5 replicas.
- 2 fs time step, or 4 fs with hydrogen mass repartitioning.
- Langevin, velocity rescale or Nosé-Hoover thermostats; Monte Carlo, stochastic cell rescaling or Parrinello-Rahman barostats; PME electrostatics.
- OpenMM or GROMACS on GPU.
Analysis and plots
- RMSD of the protein backbone and of the ligand, RMSF per residue, radius of gyration and SASA.
- Hydrogen bonds over time, protein ligand contacts and interaction fractions per residue.
- Secondary structure timeline (DSSP), ligand pose clustering, PCA and free energy landscapes.
- MM/GBSA binding energies.
- Publication ready plots as PNG, SVG or PDF, trajectories as DCD or XTC, and an optional movie.
Learn more
- How to do a molecular dynamics simulation, step by step
- Molecular docking to get the starting pose
- DFT calculations for RESP charges of unusual ligands
Need MD for your project?
Tell us the system and the length you need and we will open it for your account.