Investigating Protein Dynamics with Steered Molecular Dynamics in LAMMPS
In this lightning talk, we will introduce Steered Molecular Dynamics (SMD), a powerful technique for investigating protein dynamics and mechanical behavior. SMD applies external forces to mimic experimental stretching experiments, providing insights into protein unfolding, dissociation, ligand unbinding, and related processes.
We will briefly explain the theoretical foundation of SMD and its seamless implementation, focusing on understanding the mechanical properties of biomolecules and exploring protein dynamics. Examples of SMD applications in protein studies will be showcased.
Subsequently, we will dive into the practical side of SMD implementation in LAMMPS, a widely used molecular dynamics software. Attendees will learn how to set up SMD simulations, define pulling coordinates, and apply harmonic forces to selected atoms by using fix SMD, making the technique easily accessible for their own research.
We will also have a quick look to the post-processing tools such as VMD and python-based libraries, to interpret the simulation outputs effectively. These tools enable the generation of informative plots from LAMMPS output, enhancing the analysis of protein dynamics.