- Learning how to construct a matched pair of simulation-ready PSF/PDB files.
- Investigating simulation trajectory data.
- Displaying information contained in trajectory data in various ways, including movies.
- Introduction to MD Software: NAMD
- Some information on shells and VPN
- CHARMM-GUI NAMD
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.
In order to prepare for next week, you should look at this page: Using shells
You should also use a real plotting program. Here is qtGrace, which is a self-contained package for OS X.
CONVENTION: things you type in the terminal or tkcon are in RED. Output from the terminal, tkcon or vmd are in BLUE.