Simulation · GROMACS consortium
GROMACS
Performs molecular dynamics simulations of large biomolecular systems and membrane proteins.
What GROMACS is
GROMACS is a molecular dynamics engine developed by the GROMACS consortium for simulating the physical trajectories of biomolecules. It operates primarily on protein structures to model atomic interactions and time-dependent behaviour across defined simulation durations.
The software addresses the computational challenges associated with simulating large macromolecular assemblies. It is specifically designed to handle large systems, including membrane proteins embedded in lipid bilayers surrounded by explicit solvent environments.
Key facts
- Version
- 2024.2
- Domain
- Simulation
- Task
- Molecular dynamics
- Modalities
- Protein structure
- GPU memory
- 80 GB
What you can use it for
- Membrane Protein Simulation
- Simulates membrane-bound proteins situated in lipid bilayers to study conformational behaviour in native-like lipid environments.
- Explicit Solvent Molecular Dynamics
- Executes molecular dynamics runs for large biomolecular complexes surrounded by explicit solvent molecules.
- Production Run Trajectory Analysis
- Generates tabular trajectory analyses of macromolecular structures across specified simulation times measured in nanoseconds.
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.
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GROMACS
Strengths and limits
Good at
- Scales effectively to complete calculations on large macromolecular systems.
- Handles complex environments such as membrane proteins embedded in lipid bilayers with explicit solvent.
- Produces structured tabular trajectory analysis across the duration of a production run.
Watch out for
- Requires significant computational resources, including 80 GB of GPU memory.
- Restricted in this implementation to structural inputs provided in PDB format with simulation duration in nanoseconds.
Inputs and outputs
You provide
Structure (PDB)
Simulation length (ns)optional
You get back
Analysis over the production run.
Licence
Commercial use permitted · LGPL-2.1
The LGPL-2.1 licence allows use in commercial research and products.
Questions
Can I use GROMACS commercially?
Commercial use permitted. The LGPL-2.1 licence allows use in commercial research and products.
How do I run GROMACS 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 12h, and a run costs about 112,000 credits. Visitors without an account get 1,000 credits a month.
What inputs are required to run GROMACS?
The system requires a protein structure in PDB format and a defined simulation length specified in nanoseconds.
What biological systems is GROMACS designed to simulate?
It is suited for large biomolecular systems, particularly membrane proteins embedded in lipid bilayers surrounded by explicit solvent.
What outputs does the simulation generate?
The run outputs a trajectory table containing analysis collected over the production run.
Written from GROMACS's own documentation. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.