https://github.com/choderalab/openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
Science Score: 59.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
✓Academic publication links
Links to: acs.org, zenodo.org -
✓Committers with academic emails
3 of 39 committers (7.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.7%) to scientific vocabulary
Keywords
alchemical-free-energy-calculations
free-energy-calculations
integrators
markov-chain-monte-carlo
mcmc
molecular-dynamics
molecular-simulations
openmm
python
replica-exchange
Keywords from Contributors
molecular-dynamics-simulation
expanded-ensembles
free-energy-perturbation
molecular-design
relative-free-energy
computational-chemistry
mbar
molecular-modeling
chemistry
quantum-chemistry
Last synced: 6 months ago
·
JSON representation
Repository
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
Basic Info
- Host: GitHub
- Owner: choderalab
- License: mit
- Language: Python
- Default Branch: main
- Homepage: http://openmmtools.readthedocs.io
- Size: 33.1 MB
Statistics
- Stars: 290
- Watchers: 34
- Forks: 86
- Open Issues: 249
- Releases: 58
Topics
alchemical-free-energy-calculations
free-energy-calculations
integrators
markov-chain-monte-carlo
mcmc
molecular-dynamics
molecular-simulations
openmm
python
replica-exchange
Created over 11 years ago
· Last pushed 6 months ago
Metadata Files
Readme
Contributing
License
Code of conduct
README.md
OpenMMTools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
openmmtools is a Python library layer that sits on top of OpenMM to provide access to a variety of useful tools for building full-featured molecular simulation packages.
Features include:
- high-quality Langevin integrators, including g-BAOAB, VVVR, and other splittings
- nonequilibrium integrators for free energy calculations or nonequilibrium candidate Monte Carlo (NCMC)
- an extensible Markov chain Monte Carlo (MCMC) framework for molecular simulations
- enhanced sampling methods, including replica-exchange (REMD) and self-adjusted mixture sampling (SAMS)
- alchemical factories for generating alchemically-modified systems for absolute and relative free energy calculations
- a suite of test systems for benchmarking, validation, and debugging
- user-friendly storage interface layer
See the full documentation at ReadTheDocs.
License
OpenMMTools is distributed under the MIT License.
Contributors
A complete list of contributors can be found here.
Major contributors include:
Owner
- Name: Chodera lab // Memorial Sloan Kettering Cancer Center
- Login: choderalab
- Kind: organization
- Email: john.chodera@choderalab.org
- Location: Memorial Sloan-Kettering Cancer Center, Manhattan, NY
- Website: http://choderalab.org
- Repositories: 269
- Profile: https://github.com/choderalab
GitHub Events
Total
- Create event: 9
- Release event: 3
- Issues event: 26
- Watch event: 31
- Delete event: 8
- Issue comment event: 73
- Push event: 38
- Pull request review comment event: 16
- Pull request event: 28
- Pull request review event: 30
- Fork event: 12
Last Year
- Create event: 9
- Release event: 3
- Issues event: 26
- Watch event: 31
- Delete event: 8
- Issue comment event: 73
- Push event: 38
- Pull request review comment event: 16
- Pull request event: 28
- Pull request review event: 30
- Fork event: 12
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Andrea Rizzi | a****i@g****m | 443 |
| John Chodera | j****a@c****g | 239 |
| John Chodera (MSKCC) | c****j@m****g | 234 |
| Levi Naden | l****n@c****g | 115 |
| pgrinaway | p****y@g****m | 51 |
| kyleabeauchamp | k****p@g****m | 44 |
| adw62 | 3****2 | 39 |
| Josh Fass | j****4@c****u | 29 |
| Iván Pulido | i****o@p****m | 27 |
| Mike Henry | 1****y | 26 |
| Bas Rustenburg | b****g@c****g | 23 |
| Andrea Rizzi | a****i@c****g | 21 |
| Iván Pulido | 2****s | 17 |
| Gregory Ross | g****k@g****m | 16 |
| Andreas Krämer | k****h@g****m | 15 |
| hannahbrucemacdonald | h****d@c****g | 15 |
| Josh Fass | m****e | 12 |
| Chodera | c****j@m****g | 10 |
| Jaime Rodríguez-Guerra | j****p | 10 |
| David W.H. Swenson | d****s@h****t | 6 |
| Andy Simmonett | a****t@g****m | 5 |
| dominicrufa | d****a@g****m | 4 |
| gregoryross | G****s | 4 |
| Ivy Zhang | 3****y | 4 |
| Levi Naden | l****n@v****u | 3 |
| Jake Fennick | j****k@g****m | 3 |
| Bas Rustenburg | b****g | 3 |
| Bruce Macdonald | h****d@g****m | 3 |
| Sander Roet | s****t@h****m | 3 |
| Mark J. Williamson | m****w@m****e | 3 |
| and 9 more... | ||
Committer Domains (Top 20 + Academic)
choderalab.org: 6
lski2838.lan: 1
dhcp-204148.bio.uci.edu: 1
lilac.hpc.private: 1
mjw.name: 1
vt.edu: 1
hyperblazer.net: 1
mski1776.mskcc.root.mskcc.org: 1
cornell.edu: 1
mskcc.org: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 103
- Total pull requests: 75
- Average time to close issues: 2 months
- Average time to close pull requests: about 2 months
- Total issue authors: 43
- Total pull request authors: 17
- Average comments per issue: 1.8
- Average comments per pull request: 2.95
- Merged pull requests: 46
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 19
- Pull requests: 20
- Average time to close issues: about 2 months
- Average time to close pull requests: 12 days
- Issue authors: 13
- Pull request authors: 8
- Average comments per issue: 0.89
- Average comments per pull request: 1.3
- Merged pull requests: 12
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ijpulidos (19)
- IAlibay (11)
- jchodera (7)
- zhang-ivy (7)
- xiki-tempula (7)
- mikemhenry (5)
- mainguyenanhvu (4)
- lucl13 (3)
- Dan-Burns (3)
- yihengwuKP (2)
- schuhmc (2)
- xlimke (2)
- SHervoe-Hansen (1)
- felixmusil (1)
- chabi-fin (1)
Pull Request Authors
- ijpulidos (26)
- mikemhenry (25)
- jfennick (6)
- richardjgowers (2)
- mattwthompson (2)
- ianmkenney (2)
- IAlibay (2)
- hannahbaumann (1)
- RiesBen (1)
- dwhswenson (1)
- anyschaefer (1)
- adw62 (1)
- schuhmc (1)
- yongyouhe (1)
- dotsdl (1)
Top Labels
Issue Labels
:stars: enhancement (11)
low-effort (10)
:arrow_up: high-priority (8)
testing (5)
medium-priority (5)
:bug: bug (5)
:books: documentation (5)
medium-effort (2)
low-priority (2)
error handling (2)
api-breaking (1)
high-effort (1)
Pull Request Labels
:arrow_up: high-priority (4)
:stars: enhancement (4)
:bug: bug (2)
low-priority (2)
low-effort (1)
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 9
- Total dependent repositories: 15
- Total versions: 10
conda-forge.org: openmmtools
openmmtools is a Python library layer that sits on top of OpenMM to provide access to a variety of useful tools for building full-featured molecular simulation packages.
- Homepage: https://github.com/choderalab/openmmtools
- License: MIT
-
Latest release: 0.21.5
published over 3 years ago
Rankings
Dependent packages count: 6.5%
Dependent repos count: 9.2%
Average: 16.4%
Forks count: 21.9%
Stargazers count: 28.1%
Last synced:
6 months ago
Dependencies
.github/workflows/CI.yml
actions
- actions/checkout v1 composite
- codecov/codecov-action v1 composite
- conda-incubator/setup-miniconda v2 composite
.github/workflows/self-hosted-gpu-test.yml
actions
- actions/checkout v3 composite
- aws-actions/configure-aws-credentials v1 composite
- codecov/codecov-action v1 composite
- conda-incubator/setup-miniconda v2 composite
- machulav/ec2-github-runner main composite
docs/environment.yml
conda
- cython
- libnetcdf >=4.6.2
- mdtraj
- mpiplus
- netcdf4 >=1.4.2
- numpy
- numpydoc
- openmm >=7.3
- pymbar
- python
- pyyaml
- scipy
- setuptools
- sphinxcontrib-bibtex