├── .gitignore ├── AUTHORS.md ├── Day1-Session1-Lecture ├── Lecture1_Molecules.ipynb ├── Welcome.ipynb └── imgs │ ├── mdaclasses.png │ └── mdalogo.png ├── Day1-Session1-Practical ├── imgs │ └── adk.png └── session1_practical.ipynb ├── Day1-Session2-Lecture ├── .gitignore ├── data │ ├── TC5b.ff14igb8.HMR.parm7 │ └── TC5b.nc ├── imgs │ ├── MDA-Background.png │ ├── MDA-CoordinateReading.png │ ├── MDA-overview.png │ ├── MDA-userguide.png │ ├── mda-coordinates.png │ └── readers-writers.png └── session2-dynamics.ipynb ├── Day1-Session2-Practical ├── .gitignore ├── data │ ├── rvx-oh.dcd │ └── rvx-oh.pdb ├── figs │ └── angle_defs.png └── session2.ipynb ├── Day2-Session1-Lecture └── lib.distances.pdf ├── Day2-Session1-Practical └── day2session1-lib.distances.ipynb ├── Day2-Session2-Lecture └── universe_creation_and_manipulation-lecture.ipynb ├── Day2-Session2-Practical └── day2session2-Analysis.ipynb ├── Day3-Closing-Lecture └── MDAnalysis_Workshop_final_no_logo.pdf ├── Day3-Session1-Lecture └── MDAParallelization.pdf ├── Day3-Session1-Practical ├── .gitignore ├── README.md ├── jobscript_mpi ├── jobscript_multiprocessing ├── mpi_example.py ├── parallelism.ipynb ├── short.tpr ├── short_traj.xtc └── solution_parallelism.py ├── Day3-Session2-Lecture └── more-features.ipynb ├── Day3-Session2-Practical └── creating_and_manipulating_universes.ipynb ├── INSTALL.md ├── LICENSE.CC-BY-SA ├── LICENSE.GPLv2 ├── README.md ├── binder ├── environment.yml └── postBuild ├── environment.yml ├── figures ├── 6a_angle_def_closed.png ├── 6b_angle_def_open.png ├── HeadgroupAngle.svg ├── POPE.svg ├── angle_defs.png └── fret_distances_adk.png └── maint └── clear-practicals.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/WorkshopPrace2021/HEAD/.gitignore -------------------------------------------------------------------------------- /AUTHORS.md: 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