Molecular Modeling with VMD Tutorial

In this tutorial, we will guide you through the various steps of a molecular dynamics study using the powerful Galaxy platform. This comprehensive workflow will cover everything from accessing publicly available crystal structures to performing MD simulation and analyzing results.

Before starting, it's recommended that you have a basic understanding of the Galaxy platform and have access to a Galaxy server. You can use either the Galaxy Europe server or the Galaxy South Africa server for this tutorial. The entire analysis described in this article can be conducted efficiently on any Galaxy server with the needed tools preinstalled.

Step 1: Accessing Publicly Available Crystal Structures

In this step, we will demonstrate how to access publicly available crystal structures using Galaxy. This is a crucial step in molecular dynamics studies, as it provides valuable information about the structure of biological macromolecules such as proteins.

Step 2: Performing MD Simulation with GROMACS Engine

Once you have accessed the crystal structures, the next step is to perform MD simulation using the popular GROMACS engine. This involves setting up the simulation parameters, running the simulation, and analyzing the results.

Step 3: Analysis of Results

In this final step, we will show you how to analyze the results of your MD simulation using various tools available in Galaxy. This includes visualization of molecular structures, calculation of physical properties, and comparison with experimental data.

Throughout this tutorial, we will provide sample data, workflows, hands-on material, and references for further reading. We will also demonstrate the features of Galaxy that enable structured and reproducible high-throughput data analysis.

In conclusion, this tutorial provides a comprehensive workflow for high-throughput molecular dynamics using Galaxy, with the N-terminal domain (NTD) of Hsp90 as a case-study. By following these steps, you will gain hands-on experience in performing MD simulation and analyzing results using Galaxy.

Molecular modeling vmd tutorial