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 2 months 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 2 years ago)
• Default Branch: main
• Last Pushed: 2024-09-27T08:01:09.000Z (over 1 year ago)
• Last Synced: 2025-03-13T05:16:34.905Z (11 months ago)
• Topics: mdtraj, molecular-dynamics, scikit-learn, tutorial
• Language: Jupyter Notebook
• Homepage:
• Size: 2.88 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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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...)