e-learning
Running molecular dynamics simulations using NAMD
Abstract
In this tutorial we will perform a simulation with the popular NAMD molecular dynamics software. Please note NAMD tools are not currently available on a public Galaxy server due to licensing issues. If you are interested in following this tutorial, you will need to download the BRIDGE docker container and download NAMD yourself.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- How do I use the NAMD engine in Galaxy?
- What is the correct procedure for performing a simple molecular dynamics simulation of a protein?
Learning Objectives
- Learn about the NAMD engine provided in BRIDGE
Licence: Creative Commons Attribution 4.0 International
Keywords: Computational chemistry
Target audience: Students
Resource type: e-learning
Version: 9
Status: Draft
Prerequisites:
- Introduction to Galaxy Analyses
- Setting up molecular systems
Learning objectives:
- Learn about the NAMD engine provided in BRIDGE
Date modified: 2023-11-09
Date published: 2019-06-03
Contributors: Christopher Barnett, Simon Bray, Tharindu Senapathi
Scientific topics: Computational chemistry
Activity log
