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Introduction to MD simulation of DNA-protein systems

Tutorial PDF: 

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.

Example applications