https://github.com/uibcdf/adaptive_sampling
https://github.com/uibcdf/adaptive_sampling
Last synced: 2 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/uibcdf/adaptive_sampling
- Owner: uibcdf
- Created: 2019-05-15T03:12:35.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2020-07-08T02:39:39.000Z (almost 5 years ago)
- Last Synced: 2025-01-23T03:14:18.504Z (4 months ago)
- Language: Jupyter Notebook
- Size: 2.16 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# To have a look:
## Software
- [MSMAccelerator2](https://github.com/rmcgibbo/msmaccelerator2)
- [AdaptiveMD](https://github.com/markovmodel/adaptivemd) -see also de [documentation](https://adaptivemd.readthedocs.io/en/latest/index.html)-
- [HTMD](https://github.com/Acellera/htmd) -see also the [documentation](https://software.acellera.com/docs/latest/htmd/userguide/running.html)-
## Adaptive Sampling Explained
https://software.acellera.com/docs/latest/htmd/userguide/adaptive-sampling-explained.html
## Tutorials
https://software.acellera.com/docs/latest/htmd/tutorials/adaptive-sampling.html
## Literature
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905458/
1. S. Doerr and G. De Fabritiis. On-the-fly learning and sampling of ligand binding by high-throughput molecular simulations. Journal of Chemical Theory and Computation, 10(5):2064–2069, 2014.
2. S. Doerr, M. J. Harvey, Frank Noé, and G. De Fabritiis. HTMD: High-throughput molecular dynamics for molecular discovery. Journal of Chemical Theory and Computation, 12(4):1845–1852, 2016.
3. M. J. Harvey and G. De Fabritiis. AceCloud: Molecular dynamics simulations in the cloud. Journal of Chemical Information and Modeling, 55(5):909–914,2015.
https://aip.scitation.org/doi/10.1063/1.5053582
https://aip.scitation.org/doi/10.1063/1.4999097
https://arxiv.org/abs/1710.00495
https://www.ncbi.nlm.nih.gov/pubmed/30368832
https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.25520
## Other information sources
https://www.acellera.com/index.php/adaptive-molecular-dynamics-on-the-cloud-with-htmd-and-acecloud/