Overview

Instructor(s): Dr. Dinesh Devarajan

Time: April 2026

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.

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Course Materials

• Running Molecular Dynamics Simulations Using LAMMPS (Fall 2025): PDF

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

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