├── .gitignore ├── 01_introduction ├── 01_introduction.ipynb ├── 01_introduction.md ├── 02_molecular_setup.ipynb ├── 02_molecular_setup.md ├── 03_molecular_dynamics.ipynb ├── 03_molecular_dynamics.md ├── 04_writing_nodes.ipynb ├── 04_writing_nodes.md ├── 05_running_nodes.ipynb ├── 05_running_nodes.md ├── README.md ├── assets │ ├── 02_solvated.png │ ├── 03_rmsd.png │ ├── 03_time_series.png │ ├── 03_view_molecule.png │ ├── 03_view_molecules.png │ ├── 03_view_system.png │ ├── 04_gui.png │ └── output.zip ├── get_tutorial.py ├── myconfig │ ├── Process.py │ └── Protocol.py ├── nodes │ ├── equilibrate.ipynb │ ├── equilibrate.py │ ├── minimise.ipynb │ ├── minimise.py │ ├── parameterise.ipynb │ ├── parameterise.py │ ├── solvate.ipynb │ └── solvate.py └── scripts │ └── workflow.sh ├── 02_funnel_metad ├── 01_bss-fun-metad-setup.ipynb ├── 01_bss-fun-metad-setup.md ├── 02_bss-fun-metad-analysis.ipynb ├── 02_bss-fun-metad-analysis.md ├── README.md ├── example_nodes │ ├── equilibrate_no_trj.py │ ├── fun_metad.py │ ├── minimise.py │ ├── parameterise_solvate.py │ └── submit.sub ├── figures │ ├── figure1.jpeg │ ├── figure2.png │ └── fun-hsp90.png └── get_tutorial.py ├── 03_steered_md ├── 01_setup_sMD.ipynb ├── 01_setup_sMD.md ├── 02_trajectory_analysis.ipynb ├── 02_trajectory_analysis.md ├── README.md ├── figures │ ├── COLVAR_all.png │ ├── COLVAR_failed.png │ ├── COLVAR_snapshots.png │ ├── ensemble-md-protocol.png │ ├── open-close.png │ ├── phe196.png │ └── tyr152.png ├── get_tutorial.py └── scripts │ ├── sMD_LSF.sh │ ├── sMD_multiCV.py │ ├── sMD_simple.py │ ├── sMD_slurm.sh │ ├── seededMD.py │ └── seededMD_LSF.sh ├── 04_fep ├── 01_intro_to_alchemy │ ├── alchemical_introduction.ipynb │ ├── alchemical_introduction.md │ ├── example_output │ │ ├── mbar_bound_output.txt │ │ └── mbar_free_output.txt │ ├── get_tutorial.py │ ├── images │ │ ├── MCS.png │ │ ├── Therm_cycle.png │ │ ├── overlap_MBAR_example.png │ │ ├── overlap_MBAR_example_circles.png │ │ ├── overlap_MBAR_example_less.png │ │ ├── overlap_MBAR_example_less_circles.png │ │ └── thermo_cycle_rel_eq.png │ └── slides │ │ └── CCPBioSimTraining2022_slides.pdf ├── 02_RBFE │ ├── 01_setup_rbfe.ipynb │ ├── 01_setup_rbfe.md │ ├── 02_analysis_rbfe.ipynb │ ├── 02_analysis_rbfe.md │ ├── get_tutorial.py │ ├── images │ │ ├── fep_pipeline.png │ │ └── tyk2_protlig.png │ └── scripts │ │ ├── .svn │ │ ├── entries │ │ ├── format │ │ ├── pristine │ │ │ ├── 01 │ │ │ │ └── 015f3293a2b13c2bb141480cf0a46d2710d7e505.svn-base │ │ │ ├── 09 │ │ │ │ └── 09b149f7700b981e3a51dbb930632c234a099ab8.svn-base │ │ │ ├── 4c │ │ │ │ └── 4cdea129ef2fd591a19b69c88e8b8182b9c293ce.svn-base │ │ │ ├── e4 │ │ │ │ └── e489348848a63603fd82f847f97faf1e5598002c.svn-base │ │ │ ├── ec │ │ │ │ └── ec0594e6d6479b8b830af7315ad23adaed62f79e.svn-base │ │ │ ├── f3 │ │ │ │ └── f3791f681e50dd384968ce79e03b599e355721aa.svn-base │ │ │ └── f9 │ │ │ │ └── f9f96d03b0f2df3f8a8ec74555fbfc2374e949d6.svn-base │ │ ├── wc.db │ │ └── wc.db-journal │ │ ├── analysis.py │ │ ├── extract_execution_model_bash.sh │ │ ├── fepprep.py │ │ ├── ligprep.py │ │ ├── run_all_slurm.sh │ │ ├── run_analysis_slurm.sh │ │ ├── run_fepprep_slurm.sh │ │ ├── run_ligprep_slurm.sh │ │ └── run_production_slurm.sh ├── 03_ABFE │ ├── 01_setup_abfe.ipynb │ ├── 01_setup_abfe.md │ ├── 02_analysis_abfe.ipynb │ ├── 02_analysis_abfe.md │ ├── get_tutorial.py │ └── images │ │ ├── MCS.png │ │ ├── abfe_cycle_details.png │ │ ├── alt_poses.png │ │ ├── boresch_dof.png │ │ ├── boresch_restr_2.png │ │ ├── convergence_equil.png │ │ ├── convergence_no_equil.png │ │ ├── mif_mif180.png │ │ ├── ngl_1.png │ │ ├── ngl_2.png │ │ ├── ngl_new_1.png │ │ ├── ngl_new_2.png │ │ ├── ngl_new_3.png │ │ ├── overlap.png │ │ └── pmf_evolution.png ├── 04_PFEP │ ├── 01_setup_pfep.ipynb │ ├── 01_setup_pfep.md │ └── images │ │ └── pfep_tutorial_tcycle.png ├── 05_ATM │ ├── 01_ATM.ipynb │ └── get_tutorial.py └── README.md ├── LICENSE ├── LIVECOMS ├── 01_introduction │ └── livecoms.tex ├── 02_funnel_metad │ ├── fun-hsp90-analyses.png │ ├── funmetad-hsp90.png │ ├── funmetadfig1.jpeg │ └── livecoms.tex ├── 03_steered_md │ ├── COLVAR_all.png │ ├── ensemble-md-protocol.png │ ├── livecoms.tex │ ├── msm-final.png │ └── open-close.png ├── 04_fep │ ├── abfe-tutorial.png │ ├── alignment_visualisation.png │ ├── introfep.png │ ├── introfep_updated.png │ ├── livecoms.tex │ ├── pfep-tutorial_tcycle.png │ ├── rbfe-analysis.png │ └── rbfe-setup.png ├── livecoms.cls ├── main.tex ├── references.bib └── vancouver-livecoms.bst ├── README.md ├── Style_guide.ipynb └── releases ├── LiveCoMS_Article_v1.pdf └── header_v1.jpg /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | .ipynb_checkpoints 3 | -------------------------------------------------------------------------------- /01_introduction/01_introduction.ipynb: -------------------------------------------------------------------------------- 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