https://github.com/bio-phys/kinetics-remd
Extracting kinetics from replica exchange molecular dynamics and related methods that produce discontinuous trajectories.
Science Score: 23.0%
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 3 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 2 committers (50.0%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (4.4%) to scientific vocabulary
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Repository
Extracting kinetics from replica exchange molecular dynamics and related methods that produce discontinuous trajectories.
Basic Info
- Host: GitHub
- Owner: bio-phys
- License: bsd-3-clause
- Language: Jupyter Notebook
- Default Branch: master
- Size: 292 MB
Statistics
- Stars: 5
- Watchers: 3
- Forks: 4
- Open Issues: 1
- Releases: 0
Topics
Metadata Files
README.md
kinetics-remd
Extracting kinetics from replica exchange molecular dynamics and related methods that produce discontinuous trajectories.
Kinetics from Replica Exchange Molecular Dynamics Simulations, L.S. Stelzl and G. Hummer 2017, J. Chem. Theory Comput. http://dx.doi.org/10.1021/acs.jctc.7b00372
The repository provides two examples for extracting kinetics from replica exchange molecular dynamics (REMD):
(1) Extracting kinetics from REMD simulations of alanine dipeptide (Ala2) and comparison to MD. Importantly the ala2-lag-time folder contains everything needed to validate the generated model. This is especially important in the typical use case, when no long equilibrium MD simulations are available.
(2) Extracting kinetics from REMD simulations of a coarse-grained polymer model of the neomycin riboswitch. The extracted kinetics is compared to long MD simulations.
Owner
- Name: bio-phys
- Login: bio-phys
- Kind: organization
- Repositories: 14
- Profile: https://github.com/bio-phys
GitHub Events
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Last Year
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Lukas Stelzl | l****l@b****e | 11 |
| lukas-stelzl | l****l | 7 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 2 years ago
All Time
- Total issues: 1
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- sergiocruzleon (1)