Setting Up Molecular Dynamics Simulations
Overview
Instructor(s): Dr. James Mao
Time: April 2026
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.
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Course Materials
Participation
During the training, attendees are expected to log in to an HPRC cluster using their own computer and complete the instructor-led examples and exercises.
Learning Objectives and Agenda
In this course, participants will:
- Use CHARMM-GUI to prepare molecular dynamics (MD) systems, including setting up and performing minimization, heating, and equilibration steps.
- Modify input scripts generated by CHARMM-GUI to conduct production MD simulations on the HPRC cluster using Amber, GROMACS, NAMD, and CHARMM.