workshop_OpenMM

OpenMM workshop

HowTo

Start tutorials

If nglview does not show anything start jupyter-notebook with

jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000

Install environment

If you have anaconda just run the following commands, otherwise download ANACONDA or miniconda (e.g see below).

bash install_workshop.sh

or type

source ~/anaconda3/bin/activate
conda create -n OPS -c omnia openpathsampling nbconvert notebook &
                    -c conda-forge jupyter_nbextensions_configurator jupyter_contrib_nbextensions
conda activate OPS

# activate javascript
jupyter nbextension install widgetsnbextension --py --sys-prefix
jupyter-nbextension enable --py --sys-prefix widgetsnbextension
jupyter-nbextension enable nglview --py --sys-prefix

or us the conda_env.yml with

source ~/anaconda3/bin/activate
conda env create -n OPS -f conda_env.yml
conda activate OPS

echo $CONDA_PREFIX

# activate javascript
jupyter nbextension install widgetsnbextension --py --sys-prefix
jupyter-nbextension enable --py --sys-prefix widgetsnbextension
jupyter-nbextension enable nglview --py --sys-prefix

Install Miniconda

# For Mac OS X, substitute `MacOSX` for `Linux` below
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash -b ./Miniconda3-latest-Linux-x86_64.sh -p $HOME/miniconda

create slides

jupyter-nbconvert --to slides --post serve Untitled.ipynb

Info

see OpenMM_informations.md