e-learning
Running molecular dynamics simulations using GROMACS
Abstract
Molecular dynamics (MD) is a method to simulate molecular motion by iterative application of Newton's laws of motion. It is often applied to large biomolecules such as proteins or nucleic acids.
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 GROMACS engine in Galaxy?
- What is the correct procedure for performing a simple molecular dynamics simulation of a protein?
Learning Objectives
- Learn about the GROMACS engine provided via Galaxy.
- Understand the structure of the molecular dynamics workflow.
- Prepare a short (1 ns) trajectory for a simulation of a protein.
Licence: Creative Commons Attribution 4.0 International
Keywords: Computational chemistry
Target audience: Students
Resource type: e-learning
Version: 15
Status: Active
Prerequisites:
Introduction to Galaxy Analyses
Learning objectives:
- Learn about the GROMACS engine provided via Galaxy.
- Understand the structure of the molecular dynamics workflow.
- Prepare a short (1 ns) trajectory for a simulation of a protein.
Date modified: 2023-11-09
Date published: 2019-06-03
Contributors: Simon Bray
Scientific topics: Computational chemistry
External resources:
Activity log
