Overview

Instructor(s): Lisa M. Pérez

Time: Friday, April 9, 2021 — 1:30PM-4:00PM CT

Location: Zoom session only

Prerequisite(s): Active HPRC account

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.

Course Materials

• Classical Molecular Dynamics with NAMD (Spring 2021):
  Presentation (PDF)
  Tutorial (PDF)
• Classical Molecular Dynamics with NAMD (Spring 2020): 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.