Gromacs Tutorial

This tutorial will guide you through the setup and execution of a molecular dynamics simulation. You should have a basic understanding of working with the command line, preferably with bash under linux.

Introduction

Our starting point is a small peptide named [KIGAKI]3 in reference to its amino acid sequence. [KIGAKI]3 is a model peptide for protein aggregation in the presence of membranes. It possesses no defined secondary structure in solution but adopts a conformation that appears to maximize amphipathic character upon interacting with lipid bilayers. It possesses a large positive charge and therefore it interacts strongly with the negative charged headgroups of membrane lipids. [KIGAKI]3 was designed to form β-sheets when bound to membranes. [KIGAKI]3 is used in this tutorial, as it is a small peptide with interesting behaviour and larger proteins would take too much time to simulate for a short tutorial session. More info on [KIGAKI]3.

KIGAKI conformations
[KIGAKI]3 conformations. From left to right the peptide is shown in a (slightly unphysical) fully extended conformation, as well as more collapsed conformations adobted after some simulation time.

Learn more about the software we are going to use (popup).

Outline

This tutorial will guide you through several stages needed to perform a molecular dynamics (MD) simulation, from the initial setup to the final data anlysis.

Feedback

This tutorial is relatively new and has not been tested much in real life learning situation. Therefore we have to rely on your feedback to improve it. Please take a few minutes at the end to send some words of feedback about problems you encountered, or things you did not like by e-mail to Oliver Schillinger.