README

This is the GROMACS Umbrella sampling tutorial for the BioExcel summer school.
All files needed to perform the simulations and analyse the data can be found
in the folder 0-files. The actual tutorial is performed through the jupyter notebook
found in the main folder here.

During the tutorial you will perform the setup for a number of small simulations
to prepare Umbrella sampling on the intermolecular distance between two pyrimidine
molecules in water. The result from the analysis of those simulations will be the
potential of mean force for moving the molecules together.

The input files and simulation setup are based on tutorials available from
both Justin Lemkul (Link here please) and James W. Barnett (Link here as well).
The information from those tutorials has been updated for the current GROMACS master
branch and to use the different molecule.

If you just want to get started with running the tutorial, start the jupyter notebook
in the folder and let it guide you through the process.

The underlying python scripts used to set up files and run several simulations can be
found in the main folder under 1-python.

Happy simulation! :)