GROMACS tutorial: AWH basic: Potential of Mean Force and Convergence Assessment

Here we learn step-by-step how to sample the aggregation between two pyrimidine molecules using AWH. This simple system allows us to explore AWH using limited computational resources, but still captures much of the essential complexity that characterises real, scientific, problems. Similarly to the umbrella sampling GROMACS tutorial, we will use the pulling code to bring the two pyrimidine molecules together in an aqueous solution and then compare our estimate of the free energy of binding with the results from the umbrella sampling tutorial.