Overview: Are you interested in computing free energy using alchemical transformations? Here we give an introduction to free energy calculation in GROMACS. In this course, we focus on two methods to calculate the free energy associated with an alchemical transformation: Bennett acceptance ratio method (BAR) and accelerated weighted histogram (AWH).  The tutorials are implemented in Jupyter notebook and cover how to perform a simple alchemical transformation and compute the associated free energy change (e.i solvation free energy) using the two approaches in GROMACS 

Audience: These sessions are aimed at people interested in:
1) Starting to compute free energy using GROMACS.
2) Understanding the difference between the approaches available in GROMACS for alchemical transformation. 

Pre-requisites: A minimum knowledge of thermodynamics and minimum expertise in using GROMACS to perform Molecular Dynamics calculation are needed to attend the training.  Moreover, minimum Linux skills are also required. Please consult the following materials, if you’re uncertain of your Linux, GROMACS and Jupyter notebook skills:

• GROMACS tutorial on ​​Introduction to Molecular Dynamics 
• Linux commands, bash shell, a quiz and a link to intro course 
• A short guide to Jupyter Notebook 

Learning outcomes: At the end of these sessions, you will be able to

• describe the principles behind Bennett acceptance ratio  (BAR) and accelerated weighted histogram (AWH) methods to calculate the free energy difference associated with an alchemical transformation. 
• set up and perform simple alchemical transformations using GROMACS 
• explain which approach you can apply to your research problem