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Simulation · Chodera Lab / Stanford

OpenMM

GPU-native molecular dynamics simulation engine with a scriptable Python API for biomolecular systems.

Run it online

What OpenMM is

OpenMM is a molecular dynamics engine developed by the Chodera Lab and Stanford. It is designed to perform biomolecular simulations natively on modern graphics processing units (GPUs) and provides a scriptable Python application programming interface.

The engine is applied in structural biology and computational chemistry workflows, notably for equilibrating molecular systems ahead of free energy calculations and for testing the conformational stability of designed macromolecular structures.

Key facts

Version
8.1
Domain
Simulation
Task
Molecular dynamics
Modality
Protein structure
GPU memory
24 GB

What you can use it for

Equilibration before free energy work
Relaxes and equilibrates macromolecular systems to prepare stable starting conformations for downstream free energy calculations.
Conformational stability assessment
Simulates structural designs across specified durations to observe whether candidate conformations remain stable or unfold.
Trajectory metric analysis
Tracks frame-by-frame structural deviations, compaction through radius of gyration, and system energies over the simulation run.

Run it here

No installation and no GPU of your own: fill in the inputs and it runs on our servers. Results stay in your browser unless you sign in.

Runs on On-demand GPU

Runs on our servers with on-demand compute. A first run needs time to load the model; active capacity can be reused and scales down when idle.

Run this model

OpenMM

Needs structure (pdb)

Strengths and limits

Good at

  • Runs natively and quickly on modern GPU architectures.
  • Provides a fully scriptable Python interface for configuring simulation workflows.
  • Generates both detailed tabular trajectory metrics and all-atom coordinate files in PDB format.

Watch out for

  • Requires 24 GB of GPU memory.
  • Simulation inputs are limited to PDB structures, user-specified run lengths in nanoseconds, and supported force fields.

Inputs and outputs

You provide

  • Structure (PDB)

  • Simulation length (ns)optional

    What fits depends on the system; ask for more than fits and the answer says how much does.

  • Force fieldoptional

You get back

  • Frame-by-frame RMSD, radius of gyration and energy.

  • All-atom coordinates in PDB format, viewable and downloadable.

Licence

Commercial use permitted · MIT

The MIT licence allows use in commercial research and products.

Questions

Can I use OpenMM commercially?

Commercial use permitted. The MIT licence allows use in commercial research and products.

How do I run OpenMM without installing anything?

Use the form under “Run it here” on this page: fill in the inputs and press Run model. It runs on our servers on 4–8× A100/H100, typically in 10min, and a run costs about 2,100 credits. Visitors without an account get 1,000 credits a month.

What inputs are needed to run a simulation?

The engine requires an input structure in PDB format, a target simulation duration in nanoseconds, and the choice of force field.

What analytical measurements does OpenMM record?

It generates a trajectory table that tracks frame-by-frame root-mean-square deviation (RMSD), radius of gyration, and system energy.

What coordinate formats are produced after simulation?

The system produces all-atom coordinates in standard PDB format, available for inspection and download.

Written from OpenMM's own documentation. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.

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