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https://github.com/matsunagalab/tutorial_analyzingmddata
Google colab notebooks for typical MD trajectory analysis routines with Python
https://github.com/matsunagalab/tutorial_analyzingmddata
mdtraj molecular-dynamics scikit-learn tutorial
Last synced: about 1 month ago
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Google colab notebooks for typical MD trajectory analysis routines with Python
- Host: GitHub
- URL: https://github.com/matsunagalab/tutorial_analyzingmddata
- Owner: matsunagalab
- License: mit
- Created: 2023-07-02T14:40:50.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2023-09-24T08:30:13.000Z (about 1 year ago)
- Last Synced: 2023-09-24T15:52:43.362Z (about 1 year ago)
- Topics: mdtraj, molecular-dynamics, scikit-learn, tutorial
- Language: Jupyter Notebook
- Homepage:
- Size: 1.47 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
Google colab notebooks for typical MD trajectory analysis routines with Python
まずはMDデータ解析の雰囲気を知るために[スパコンコロキウム](https://fugaku100kei.jp/events/colloquium/)の第4回の動画を視聴してから取り組んでください。
このチュートリアルを独習したい場合は、過去の[セミナーの動画](https://suitc.sharepoint.com/:v:/r/sites/GR_matsunagalab/Shared%20Documents/General/Recordings/%E3%82%B3%E3%83%B3%E3%83%94%E3%83%A5%E3%83%BC%E3%82%BF%E6%BC%94%E7%BF%924-20230719_150905-Meeting%20Recording.mp4?csf=1&web=1&e=S1Mx6i)(研究室内限定の公開)を視聴しながら学習してください。
## 00 Preprocess
[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/matsunagalab/md_analysis/blob/main/00_preprocess.ipynb)## 01 MDTraj basics
[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/matsunagalab/md_analysis/blob/main/01_mdtraj_basics.ipynb)## 02 MDTraj atom selection
[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/matsunagalab/md_analysis/blob/main/02_mdtraj_atomselection.ipynb)## 03 Geometry analysis
[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/matsunagalab/md_analysis/blob/main/03_md_geometry.ipynb)## 04 Superpose of trajectories
[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/matsunagalab/md_analysis/blob/main/04_md_superpose.ipynb)## 05 Dimensional reduction
[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/matsunagalab/md_analysis/blob/main/05_md_dimensionalreduction.ipynb)## 06 Clustering (on-going...)
## 07 Hydrogen bonds (on-going...)
## 08 Free energy analysis (on-going...)
## 09 Markov state modeling (on-going...)