gromacs-free-energy-tutorial

Workstation

On the workstations these can be run with the following commands

bash setup-environment.sh

source env/bin/activate

jupyter notebook

Note that on the workstations the command:

module load gromacs/2018.2

does not load gromacs but that gromacs 5.1 is in the path so the notebook should still work.

For Tegner, getting the notebook running will be more complicated, but will look something like the following.

module load anaconda/py36/5.0.1

source activate pyemma

jupyter notebook --no-browser --port=XXXX

pdc-ssh -N -L YYYY:localhost:XXXX <username>@<your assigned node>.pdc.kth.se

Name		Name	Last commit message	Last commit date
Latest commit History 12 Commits
images		images
input_files		input_files
README.md		README.md
gromacs-free-energy-tutorial.ipynb		gromacs-free-energy-tutorial.ipynb
gromacs-free-energy-tutorial.py		gromacs-free-energy-tutorial.py
requirements.txt		requirements.txt
setup-environment.sh		setup-environment.sh