Martini OpenMM Molecular Dynamics
Run Martini coarse-grained OpenMM molecular dynamics simulations with staged minimization, NVT, NPT, and production MD.
Overview
Perform coarse-grained molecular dynamics with Martini and OpenMM for protein, ligand, solvent, ion, and optional membrane systems.
Run Martini OpenMM Molecular Dynamics on Neurosnap
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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| Runtime 90th Percentile | loading... |
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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/ |
Video Tutorial
The following youtube video describes how to use Martini OpenMM Molecular Dynamics using Neurosnap's online webserver. If you have any questions or want to suggest improvements for future tutorials please contact us here.