Making it Rain: Cloud-Based Molecular Simulations for Everyone
Open accessPublished version of a preprint
Abstract
We present a user-friendly front-end for running molecular dynamics (MD) simulations using the OpenMM toolkit on the Google Colab framework. Our goals are (1) to highlight the usage of a cloud-computing scheme for educational purposes for a hands-on approach when learning MD simulations and (2) to exemplify how low-income research groups can perform MD simulations in the microsecond time scale. We hope this work facilitates teaching and learning of molecular simulation throughout the community.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Harris, C. R., Millman, K. J., van der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., Wieser, E., Taylor, J., Berg, S., Smith, N. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2649-2 · Cited by 23,826 · see citing works
ColabFold - Making protein folding accessible to all
Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2021) · doi:10.1101/2021.08.15.456425 · Cited by 9,391 · see citing works
Highly accurate protein structure prediction for the human proteome
Tunyasuvunakool, K., Adler, J., Wu, Z., Green, T., Zielinski, M., Žídek, A., Bridgland, A., Cowie, A., Meyer, C., Laydon, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03828-1 · Cited by 3,025 · see citing works
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- Authors
- Arantes, P. R., Polêto, M. D., Pedebos, C., & Ligabue-Braun, R.
- Affiliations
- University of California, Riverside (US)
- Virginia Tech (US)
- University of Southampton (GB)
- Department of Pharmacosciences, Federal University of Health Sciences of Proto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil
- Corresponding author
- Arantes, Pablo R.
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2021-10-01
- Volume
- 61
- Issue
- 10
- Pages
- 4852-4856
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W3203800312
- Cited by
- 148
- References
- 4
- Citations by year
- 2026: 47 · 2025: 30 · 2024: 27 · 2023: 30 · 2022: 14
- FWCI
- 10.77
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Journal of Chemical Information and Modeling (publishedVersion)
- ChemRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Various Chemistry Research Topics
- Physical Sciences › Computer Science › Information Systems › Innovative Educational Technologies
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Keywords
- molecular dynamics, OpenMM, Google Colab, cloud computing
- MeSH terms
- Cloud Computing, Molecular Dynamics Simulation
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