Initial Commit; Added several small scripts, including:

RMSF.tcl - Finds RMSF of a DCD simulation
RG.tcl - Find Radius of Gyration of a DCD Simulation
density-AF.tcl - Finds density of a DCD simulation (tuned for water box)
namd_plot.tcl - Graphs Values from NAMD simulation logfiles
prep.tcl - Prepares protein for simulation
RWalk.R - R Code for Random Walk (Not Optimized...)