Molecular dynamics
Runs a real GROMACS simulation on a structure, optionally with a bound ligand, and produces a trajectory the platform's own analysis tools can read directly.
Molecular dynamics
What it does
Runs a molecular dynamics simulation — a real physics simulation of atoms moving under a force field, not a static prediction — on a protein structure, optionally with a small-molecule ligand bound near it. The result is a trajectory: a record of how the system's coordinates changed over the course of the simulated time. Use it to check whether a structure (or a structure-plus-ligand complex) stays stable, and as the input to Trajectory stability and Hydrogen-bond persistence, which turn that raw trajectory into a readable answer.
How the simulation is run
The engine is GROMACS, with ACPYPE handling ligand parameterization when one is supplied. The pipeline prepares the protein, optionally parameterizes and adds the ligand, places the whole system in a water box, neutralizes it with ions, minimizes its energy, equilibrates it at constant temperature, and then runs the production simulation for the length you choose — every step using the same force field (amber99sb-ildn) and water model (tip3p) throughout.
Simulation length is yours to set, up to a limit this deployment configures. Longer runs give a more complete picture of how a structure's flexibility develops, but take proportionally longer — this platform's own testing found that the general shape of a result (which regions of a structure move the most) settles quickly, while the precise numbers keep refining the longer a simulation runs. Pick a length that matches how much precision you need.
Reading the output
Two files come back: the trajectory itself, and a reference structure from the same run. Neither is meant to be read directly — feed both into Trajectory stability (movement and stability over time) or Hydrogen-bond persistence (which contacts with a bound ligand actually hold) to get a readable answer.
Input
A structure, saved as PDB. Optionally, a small-molecule ligand, saved as SDF, to include a bound complex in the simulation.
Important limitations
A ligand is placed near the protein, not docked into it. This tool gives a supplied ligand a reasonable starting position and lets the simulation's own physics settle any initial closeness — it does not perform docking. For a scientifically meaningful bound-complex simulation, dock the ligand first (with Small-molecule docking) and use that result as this tool's ligand input.
Runs on this platform's own compute queue and can take a while. A run's progress shows in Run Results; longer simulation lengths take longer, proportionally.
No GPU acceleration. Simulations run on CPU only in this deployment.