Overview

Instructor(s): Dr. Dinesh Devarajan

Time: Friday, November 14, 2025 1:30PM-4:00PM CT

Location: Blocker 220

Prerequisite(s): Active HPRC account, basic Linux/Unix skills

This short course provides a practical, step-by-step introduction to setting up and running molecular dynamics (MD) simulations using LAMMPS on the Texas A&M High Performance Research Computing (HPRC) clusters. Participants will learn how to model a range of systems, from simple materials to biomolecules, using both all-atom and coarse-grained force fields. The course combines conceptual overviews with hands-on exercises to help users confidently run and analyze MD simulations in an HPC environment.

Course Materials

Presentation slides

Learning Objectives

In this course, participants will:

• Understand key input and data file formats (input scripts, topology/data files, force field parameters, and job submission scripts)
• Set up and execute MD simulations for energy minimization, equilibration, and production phases
• Practice modifying and adapting LAMMPS input scripts for different system types (e.g., liquids, polymers, proteins)
• Perform basic post-processing and trajectory analysis using LAMMPS outputs as well as visualize simulation trajectories

Note: Be sure to bring your computer, log in to Grace, and complete the tasks and exercises along with the instructor.