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…

• NI
  National Institute of Food and Agriculture

  Awards: VA-160092, VA-160211
• NI
  National Institute of General Medical Sciences

  Award: R35GM133754