A Suite of Advanced Tutorials for the GROMOS Biomolecular Simulation Software [v2.0]

Abstract

This tutorial describes the practical use of some recent methodological advances implemented in the GROMOS software for biomolecular simulations. It is envisioned as a living document, with additional tutorials being added in the course of time. Currently, it consists of six distinct tutorials. The first tutorial describes the use of time-averaged restraints to enforce agreement with order parameters derived from NMR experiments. The second tutorial describes the use of extended thermodynamic integration in the double-decoupling method to compute the affinity of a small molecule to a protein. The molecule involved bears a negative charge, necessitating the application of post-simulation corrections. The third tutorial is based on the same molecular system, but computes the binding free energy from a path-sampling method with distance-field distance restraints and Hamiltonian replica exchange simulations. The fourth tutorial describes the use of Gaussian accelerated MD, an enhanced sampling technique. The fifth tutorial is about the use of Accelerated Enveloping Distribution Sampling (AEDS) an enhanced version of EDS. The sixth tutorial illustrates how to run QM/MM simulations with the Buffer Region Neural Network (BuRNN) method. The tutorials are written for users with some experience in the application of molecular dynamics simulations.