Searching for the Cure – COVID-19 Classical Molecular Dynamics with NAMD

Overview

Instructor: Dr. Lisa M. Perez

Time: Friday, April 17, 10:00AM-12:30PM

Location: Zoom session only

Prerequisites: HPRC account

Course Materials

Presentation slides

The presentation slides are available as downloadable PDF files.

  • Molecular Dynamics: PDF

Agenda

This course focuses on the following topics:

  • Protein preparation for MD simulations
  • Force-fields
  • Molecular Mechanics
  • Molecular Dynamics
  • Hands-on exercises using NAMD as applied to COVID-19

This course focuses on the basic concepts behind classical Molecular Dynamics (MD) and its direct application to modeling COVID-19 using NAMD, an open-source scalable molecular dynamics code.