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Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"Google colab notebooks for typical MD trajectory analysis routines with Python\n\n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。\n\n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\u0026web=1\u0026e=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。\n\n## 00 Preprocess\n[![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)\n\n## 01 MDTraj basics\n[![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)\n\n## 02 MDTraj atom selection\n[![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)\n\n## 03 Geometry analysis\n[![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)\n\n## 04 Superpose of trajectories\n[![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)\n\n## 05 Dimensional reduction\n[![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)\n\n## 06 Clustering (on-going...)\n\n## 07 Hydrogen bonds (on-going...)\n\n## 08 Free energy analysis (on-going...)\n\n## 09 Markov state modeling (on-going...)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmatsunagalab%2Ftutorial_analyzingmddata","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmatsunagalab%2Ftutorial_analyzingmddata","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmatsunagalab%2Ftutorial_analyzingmddata/lists"}