Use Martini OpenMM Molecular Dynamics
Official Neurosnap webserver for accessing Martini OpenMM Molecular Dynamics online.
Overview
Perform coarse-grained molecular dynamics with Martini and OpenMM for protein, ligand, solvent, ion, and optional membrane systems.
Neurosnap Overview
The Martini OpenMM Molecular Dynamics online webserver allows anybody with a Neurosnap account to run and access Martini OpenMM Molecular Dynamics, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong Terms of Use and Privacy Policy.
Features
- Runs Martini coarse-grained molecular dynamics with OpenMM on CUDA GPUs.
- Supports protein structures, uploaded SDF ligands, solvent, ions, and optional Martini membrane setup.
- Automatically parameterizes small organic SDF ligands with Auto_MartiniM3 for Martini 3 jobs.
- Uses staged energy minimization, NVT equilibration, NPT equilibration, and production dynamics.
- Does not currently support protein/nucleic-acid complexes in the automated Martini workflow.
Statistics
Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.
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API Request
Access Martini OpenMM Molecular Dynamics using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.
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Citations
Please cite the original work when using Martini OpenMM Molecular Dynamics in publications or research outputs.
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Souza, P. C. T. et al. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nature Methods, 2021. https://doi.org/10.1038/s41592-021-01098-3. |
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Kroon, P. C. et al. Martinize2 and Vermouth provide a unified framework for molecular topology generation. eLife, 2024. https://doi.org/10.7554/eLife.90627.2. |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |
Job Note
Provide a name or description for your job to help you organize and track its results. This input is solely for organizational purposes and does not impact the outcome of the job.
Inputs & Configuration
Ready to submit your job?
Review your configuration, then confirm the estimated credit cost before you run the job.
Note that credit estimates are not guaranteed and runtime can vary depending on inputs and settings.
Estimated Credits: calculating...
To submit a job please login or register an account.