Overview

Instructor(s): Dr. James Mao

Time: Friday, November 14, 2025 10:00AM-12:30PM CT

Location: Blocker 220

Prerequisite(s): Active HPRC account, active CHARMM-GUI account, basic Linux/Unix skills

This short course provides a step-by-step guide to setting up molecular dynamics (MD) simulations. Participants will learn to use CHARMM-GUI to prepare molecular dynamics systems, including minimization, heating, and equilibration, before proceeding to the production phase.

The course will also cover performing production MD simulations using various software available on the HPRC cluster, including Amber, GROMACS, NAMD, and CHARMM.

Course Materials

Presentation slides

• Setting Up Molecular Dynamics Simulations (Spring 2025): [PDF]

Learning Objectives

In this course, participants will:

• Gain hands-on experience using CHARMM-GUI to prepare molecular dynamics (MD) systems, including setting up and performing minimization, heating, and equilibration steps.
• Learn how to modify input scripts generated by CHARMM-GUI to conduct production MD simulations on the HPRC cluster using Amber, GROMACS, NAMD, and CHARMM.

Note: Be sure to bring your computer, log in to Grace, and complete the tasks and exercises along with the instructor. Participants must also register for a CHARMM-GUI account to use the platform during the course. Since account approval may take up to 24 hours, registration should be completed at least one day prior to the course.