This Unit presents a series of examples of how to analyze data produced from NAMD simulations. For these examples you will not run the simulations themselves; instead you will analyze already produced data. Nevertheless, the instructions to set up and run the simulations are included, so you can actually produce the data yourself if time permits.

The steps that must be followed for the analysis are marked with an asterisk (*). Make sure to go through these steps. We encourage you to at least read the other steps, so you can refer to them later when setting up future simulations.

You will need to use software packages other than NAMD to analyze your data. Specifically, you will use:

**VMD**, a molecular graphics program. This software is also developed by the Theoretical and Computational Biophysics Group. You can download it for free from www.ks.uiuc.edu/Research/vmd. We encourage you to go through the VMD tutorial at www.ks.uiuc.edu/Research/vmd/tutorial prior to using the present tutorial.- a
**2-D plotting program**such as xmgrace, gnuplot, Matlab, Mathematica, or Excel. You will find detailed instructions to go through the exercises using xmgrace, but you are encouraged to use your preferred method. **other NAMD tools**that you can find at www.ks.uiuc.edu/Research/namd.

The exercises will have detailed explanations of methods used. We encourage, however, that you be bold and try your own way to do the analysis.

- Equilibrium
- RMSD for individual residues
- Maxwell-Boltzmann Energy Distribution
- Energies
- Temperature distribution
- Specific Heat

- Non-equilibrium properties of protein