Introduction to MD simulation of DNA-protein systems
This tutorial consists of five sections that gradually introduces the reader to Molecular Dynamics simulations as the skills and techniques needed to simulate the removal of ssDNA from single-stranded DNA binding protein are developed. The tutorial covers the basic of MD simulation,from the process of obtaining a protein model from the RCSB protein data bank to the analysis of steered MD data. Requires NAMD and VMD. Tutorial works on Mac and Unix/Linux platforms.