Molecular Dynamics on WVU Resources

This series of lessons details the steps necessary to make use of some of the most popular Molecular Dynamics (MD) simulation codes on WVU’s most recent HPC cluster, Thorny Flat.

In the lessons, there is an introduction to the concept of MD simulation, followed by an introduction to each of the codes listed here: NAMD, Gromacs, and Amber. These lessons are by no means exhaustive; there is much to learn about how each of these codes work. However, the lessons provide the essentials to making use of the computing power of Thorny Flat, ultimately accelerating your simulations. Links to more information on the codes will be provided in their respective lessons.

Prerequisites

There are no prerequisites for this course, however it will be very beneficial to go through the tutorials of the engine you’re using: NAMD, GROMACS, and AMBER.

Schedule

	Setup	Download files required for the lesson
00:00	1. Introduction: Basic introduction to MD	What is Molecular-Dynamics ?
00:15	2. Using Nanoscale Molecular Dynamics (NAMD) on WVU HPC resources	How do I transfer my files to the HPC? How do I run NAMD on the cluster? How do I check if my job has failed?
01:00	3. Using Gromacs on WVU HPC resources	What is GROMACS? How do I run GROMACS on the cluster? How do I check on my job and the simulation status?
01:00	4. Using AMBER on WVU HPC resources	How do I transfer my files to the HPC? How do I run NAMD on the cluster? How do I check if my job has failed?
01:00	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.