(This assignment is worth DOUBLE POINTS - 40! Due Saturday Aug. 14, 12:00 AM/Midnight)
  1. Using one of the proteins mentioned in the Vacuum MD exercise, prepare and run a vacuum simulation. Remember to extract any extraneous molecules (ligands, waters, ions) and either remove them or put them into their own segment (if you include a separate segment in this way, you will receive bonus points). Run 2000 minimization steps and 10,000 MD steps at 310 K. The files you need to save to your DropBox:
    1. The PSF file
    1. The PDB file
    1. The DCD file
    1. The control file (.nam)
  1. Using your DCD File, above, perform two types of analysis on your data. These may include:
    1. energy versus time plot
    1. RMSD versus experimental structure plot
    1. RDF plot (be sure to clearly specify what atoms, etc are the subject of the plot!)
  1. Files required to be saved to BioFS include the data file, and either a plot or a screen shot of the VMD plot of the data.