Resources

This index is updated automatically with the scripts and notebooks used in the course.

Python scripts

Script	Download	Page
`01-introduccion.py`	Download	Episode 1 - Introduction (environment and data)
`01-introduccion_simple.py`	Download	Episode 1 - Introduction (environment and data)
`02-preparacion-sistema.py`	Download	Episode 3 - Preparing and editing the system in OpenMM
`02-preparacion-sistema_simple.py`	Download	Episode 3 - Preparing and editing the system in OpenMM
`03-simulaciones-clasicas.py`	Download	Episode 2 - Running simulations
`03-simulaciones-clasicas_simple.py`	Download	Episode 2 - Running simulations
`04-analisis-trayectorias.py`	Download	Episode 5 - Trajectory analysis with MDTraj
`04-analisis-trayectorias_simple.py`	Download	Episode 5 - Trajectory analysis with MDTraj
`04-gamd.py`	Download	Episode 4 - Advanced sampling and mathematical foundations
`04-martini-complex.py`	Download	Episode 4 - Advanced sampling and mathematical foundations
`04-remd.py`	Download	Episode 4 - Advanced sampling and mathematical foundations
`05-muestreo-avanzado.py`	Download	Episode 4 - Advanced sampling and mathematical foundations
`05-muestreo-avanzado_simple.py`	Download	Episode 4 - Advanced sampling and mathematical foundations
`06-pyemma-pentapeptide.py`	Download	Episode 6 - MSMs with PyEMMA
`course_paths.py`	Download	Episode 3 - Preparing and editing the system in OpenMM
`openmm_advanced_annealing.py`	Download	Episode 4 - Advanced sampling and mathematical foundations
`openmm_advanced_compute_energies.py`	Download	Unassigned
`openmm_advanced_force_reporter.py`	Download	Unassigned
`openmm_advanced_spherical.py`	Download	Unassigned
`openmm_modeller_save.py`	Download	Episode 3 - Preparing and editing the system in OpenMM
`openmm_running_amber.py`	Download	Episode 2 - Running simulations
`openmm_running_charmm.py`	Download	Episode 2 - Running simulations
`openmm_running_gromacs.py`	Download	Episode 2 - Running simulations
`openmm_running_pdb.py`	Download	Episode 2 - Running simulations
`openmm_running_tinker.py`	Download	Episode 2 - Running simulations

Jupyter notebooks

Notebook	View	Download	Page
`01-introduccion-protein2-ligand-nglview.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`01-introduccion-protein2-nglview.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`01-introduccion-protein2-protein-nglview.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`01-introduccion.ipynb`	View (nbviewer) View (HTML)	Download	Episode 1 - Introduction (environment and data) Notebooks
`01-introduccion_simple.ipynb`	View (nbviewer) View (HTML)	Download	Episode 1 - Introduction (environment and data) Notebooks
`01-introduction-ligand-check.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`01-introduction-sequence-check.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`02-preparacion-sistema.ipynb`	View (nbviewer) View (HTML)	Download	Episode 3 - Preparing and editing the system in OpenMM Notebooks
`02-preparacion-sistema_simple.ipynb`	View (nbviewer) View (HTML)	Download	Episode 3 - Preparing and editing the system in OpenMM Notebooks
`02-trajectory-rg.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`02-trajectory-rmsd.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`02-trajectory-rmsf.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`03-simulaciones-clasicas.ipynb`	View (nbviewer) View (HTML)	Download	Episode 2 - Running simulations Notebooks
`03-simulaciones-clasicas_simple.ipynb`	View (nbviewer) View (HTML)	Download	Episode 2 - Running simulations Notebooks
`03-trajectory-rg.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`03-trajectory-rmsd.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`03-trajectory-rmsf.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`04-gamd.ipynb`	View (nbviewer) View (HTML)	Download	Episode 4 - Advanced sampling and mathematical foundations Notebooks
`04-martini-complex.ipynb`	View (nbviewer) View (HTML)	Download	Episode 4 - Advanced sampling and mathematical foundations Notebooks
`04-muestreo-avanzado.ipynb`	View (nbviewer) View (HTML)	Download	Episode 4 - Advanced sampling and mathematical foundations Notebooks
`04-muestreo-avanzado_simple.ipynb`	View (nbviewer) View (HTML)	Download	Episode 4 - Advanced sampling and mathematical foundations Notebooks
`04-remd.ipynb`	View (nbviewer) View (HTML)	Download	Episode 4 - Advanced sampling and mathematical foundations Notebooks
`04-simulated-annealing.ipynb`	View (nbviewer) View (HTML)	Download	Episode 4 - Advanced sampling and mathematical foundations Episode 5 - Trajectory analysis with MDTraj Notebooks
`05-analisis-trayectorias.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`05-analisis-trayectorias_simple.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`05-umbrella-sampling.ipynb`	View (nbviewer) View (HTML)	Download	Episode 4 - Advanced sampling and mathematical foundations Notebooks
`06-pyemma-pentapeptide.ipynb`	View (nbviewer) View (HTML)	Download	Episode 6 - MSMs with PyEMMA Notebooks
`07-deeptime-ala2.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`07-deeptime-alanine.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks
`07-deeptime-complex.ipynb`	View (nbviewer) View (HTML)	Download	Notebooks