├── .github ├── dependabot.yml └── workflows │ └── build.yaml ├── .gitignore ├── AUTHORS ├── LICENSE ├── README.md ├── _config.yml ├── data ├── CHO.frcmod ├── CHO.prepc ├── cm_md.pdb ├── make_adiab_trj.in ├── make_us_trj.in ├── md1.rst ├── md10.rst ├── md11.rst ├── md12.rst ├── md13.rst ├── md14.rst ├── md15.rst ├── md16.rst ├── md17.rst ├── md18.rst ├── md19.rst ├── md1ps.i ├── md2.rst ├── md20.rst ├── md3.rst ├── md4.rst ├── md5.rst ├── md6.rst ├── md7.rst ├── md8.rst ├── md9.rst ├── min_init.i ├── min_xmin3_temp.i ├── rc_temp.RST ├── strip_arg90.in ├── tleap_box.in └── wt.sp20.top ├── docker ├── Dockerfile └── default-37a8.jupyterlab-workspace ├── example ├── adiab_traj.mdcrd ├── example.xlsx ├── us_traj.mdcrd ├── view_traj.vmd └── wt.box.top ├── pics ├── TSpic.jpg ├── adiab.png ├── chorismate.jpg ├── chorismate_reaction.png ├── pmf.png └── reaction_profile.png ├── qmmm_intro2019.pdf ├── qmmm_workshop.ipynb ├── qmmm_wrap2019.pdf ├── requirements.txt └── scripts ├── run_adiab_all.sh 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