The purpose of this workshop is to acquaint you with the basics of molecular modeling and what is needed to perform modeling in the InsightII graphical user environment. The example we will be using is the Cytochrome C protein (entry 5cyt.pdb in the Brookhaven Protein Data Bank)

During this workshop you will:

• learn to "read" a PDB file;
• what a forcefield is and what type of forcefields exist;
• learn what a simulation engine is;
• prepare your system for molecular dynamics;
• do minimization for your system;
• set up a molecular dynamics run;
• read the results of a MD run and display them