settingup.md

Setting up software for the material from this i-CoMSE workshop:

If you are participating in the workshop with Bridges2 on PSC

Running this command on Bridges2 will set up singularity images that can be used in jupyter notebooks through OnDemand:

bash /ocean/projects/see220002p/shared/icomse-setup.sh

If you don't have an account on PSC

Most of the workshop functionality is provided through python libraries. If you wish to replicate the python environment from the container locally without gromacs use this environment.yml:

conda env create -f environment.yml
conda activate icomseW23

And to get gromacs/plumed via conda:

	conda install --strict-channel-priority -c \
	    plumed/label/masterclass-2022 -c conda-forge plumed gromacs