(This assignment is worth DOUBLE POINTS - 40! Due Saturday July 4, 12:00 AM Midnight)

  • 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:
    • The PSF file
    • The PDB file
    • The DCD file
    • The control file (.nam)
  • Using your DCD File, above, perform two types of analysis on your data. These may include:
    • energy versus time plot
    • RMSD versus experimental structure plot
    • RDF plot (be sure to clearly specify what atoms, etc are the subject of the plot!)
  • 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.