Introductory Tutorials for Simulating Protein Dynamics with GROMACS

Atomistic molecular
dynamics (MD) simulations have become an indispensable
tool for investigating the structure, dynamics, and energetics of
biomolecules. Continual optimization of software algorithms and hardware
has enabled investigators to access biologically relevant time scales
in feasible amounts of computing time. Given the widespread use and
utility of MD simulations, there is considerable interest in learning
essential skills in performing them. Here, we present a set of introductory
tutorials for performing MD simulations of proteins in the popular,
open-source GROMACS package. Three exercises are detailed, including
simulating a single protein, setting up a protein complex, and performing
umbrella sampling simulations to model the unfolding of a short polypeptide.
Essential features and input settings are illustrated throughout.
The purpose of these tutorials is to provide new users with a general
understanding of foundational workflows, from which they can design
their own simulations.