Updated July 14, 2022.
Pulling data: PSF File/DCD File
Butane: PSF PDB DCD
(right-click on these links and "save as" to your hard drive)
FileSet2
1. Using the pulling data (links above), measure the distance from one end of the peptide to the other as a function of time. Where does the pulling occur within the peptide? Try to plot your data so that this question is answered clearly. (10 Points)
2. Make a movie of a trajectory. Choose one of the trajectories provided to do this. You may do one of two things:
A) If you choose the Butane trajectory, pick one particular butane molecule and differentiate it clearly by using a singular representation (a simple example would be making one butane a VdW representation, while every other butane is CPK; however there is probably a better way to do this).
B) If you choose a peptide trajectory, pick one residue (lysine or cysteine or...) and isolate it by representation (as above).