During the last week, you will work on a full simulation, from downloading, preparing, running, and analysis. It is a good idea to choose a protein from the RCSB or the class list early (during the second week?), and work with it as you do the other assignments. This page will offer some suggestions.
- Pulling (SMD) simulation. If you choose a pulling simulation, you must average the results of (at least) five separate runs.
- Solvated protein. In this case, you must solvate your protein of choice in a water box and do some analyses
- Other possibilities…?