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====== Ramachandran Analysis ======


This analysis will create a Ramachandran plot for your peptide system in any range of trajectory files you desire.

All scripts necessary can be found in the following path in DT2:

/lustre/tcline/rama-analysis

=== Gathering the phi-psi data ===

    - Copy the tcl script "phipsi.txt" to your directory with the trajectory files you want to analyze.
  -  Open the script to see the arguments necessary [start] [end] [filename] [output file name]
  -  You may need to adjust the lines including the .psf and the .dcd file names to your system
  -  Load the module vmd on the command line by typing "module load vmd" (this is not done on your computer at home but on the resource you are using)
  -  If this does not work, check what the vmd module is by typing "module avail" and then loading the appropriate vmd module
  -  Once inside of the VMD application, load the tcl script by typing "source phipsi.txt"
  -  Then type "phipsi [start] [end] [filename] [output file name]"
  -  Once it completes, you can check with the example output to see if it matches the format; example output found at the path:
 /lustre/tcline/rama-analysis/ex-output

=== Matlab Analysis ===

  - Once you have gathered all the data files you want for the blocks of trajectory files desired, transfer all of these data files to your home computer that has Matlab
  -  In Matlab you'll upload "ramaplot.m" and navigate the working directory to the path where all your data files are
  -  You'll need to edit the ~file~ variable containing the names of all the data files
  -  Likewise, change the name of the plot titles to match the order of your data files in the variable ~titlelist~
  -  Example output of the plots is found in the example output folder listed above 

=== Group of 4 residue analysis ===

  - This analysis used the Matlab script "ResidGroupAnalysis.m"
  - As with the standard analysis, you'll need to adjust the ~file~ and ~titlelist~ variables
  - You also need to adjust the number of residues in your peptide with the variable ~residues~
  - The article [[https://www.sciencedirect.com/science/article/pii/S1359027896000466]] shows the effectiveness of using this group analysis compared to standard per residue Ramachandran plots
  - Example output data is also found in the directory listed above