First Molecular Dynamic Simulation
Step-1. Introduction

Pietro Buffa

GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package originally developed in the University of Groningen. This tutorial assumes that GROMAS 4.x is correctly installed on your own system. For this tutorial we are going to use the protein lysozyme as an example. Go to the Research Collaboratory for Structural Bioinformatics (RCSB) website and download the PDB crystal structure file for this protein (PDBcode: 1AKI). Lysozyme is an enzyme which functions to hydrolyze the &beta(1-4) glycosidic bond between residues of N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) in certain polysaccharides. Lysozyme consists of a single polypeptide chain of 129 amino acid residues. It has an alpha+beta fold, consisting of five to seven alpha helices (depending on the species) and a three-strands antiparallel beta sheet. The enzyme is approximately ellipsoidal in shape, with a large cleft in one side forming the active site (a model is dispayed on the left). Once you downloaded the file, you can visualize the structure using different viewing programs like: VMD, Chimera, Pymol etc. In this example, we want the protein to be free from other molecules. Use a text editor to check the presence of water molecules and/or other and delete the lines corresponding to these molecules. Such a procedure is not universally appropriate but our intention here is to have a free protein. Always check your PDB file in order to find missing regions into the protein or missing atoms. Incomplete internal sequences or even amino acid residues with missing atoms will cause a problem. If so, you have to model them using other software packages before starting this tutorial.

Molecular Dynamic Simulation is a really complex field so, you have to consider this tutorial as an introduction. If you want to know more about it, we recommend you to read the GROMACS guide and the GROMACS documentation that you can find into the offical GROMACS web site: Online Documentation / Official Manual

Go to the Step-2.