Overview

Instructor: Michael Dickens

Time: Tuesday, March 5, 2024 — 1:30PM-4:00PM CT

Location: Online using Zoom

Prerequisites: Current ACCESS ID, basic Linux/Unix skills

This short course covers how to run AlphaFold on the ACES cluster, utilizing the NVIDIA H100 GPUs.

Course Materials

Presentation slides

The presentation slides will be made available as downloadable PDF files.

• AlphaFold Protein Structure Prediction (Spring 2024): PDF

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Agenda

This course focuses, among others, on the following topics:

• Resources and Limitations
• Database Files
• Running AlphaFold
• Grace GPU or non-GPU nodes
• Visualization of Results
  • job resource usage
  • plotting pLDDT values
• Alternative Workflows

Note: During the class sessions many aspects of the material will be illustrated live via a login to Grace. Attendees will follow along and complete the exercises on their own laptops. They will need to configure their laptops to use the TAMULink wireless network. Relevant details on this can be found at: http://tamulink.tamu.edu

You are encouraged to contact the HPRC helpdesk with any questions regarding Grace.