- 1UBQ.pdb: PDB file of ubiquitin protein

- coloring.tcl: Computes distance between atoms of two 
selections and then assigns the distance to beta values of the crystal 
molecule.

- equilibration.dcd: trajectory of an equilibration 

- pulling.dcd: trajectory of an SMD simulation in which one end of the 
protein is being pulled while the other is kept fixed.

- rmsd-fullthrottle.tcl: computes rmsd per residue.

- rmsd.tcl: computes root mean squeare deviation.

- ubiquitin-equilibrated.coor: coordinates of ubiquitin equilibrated.

- ubiquitin.psf: structure file for ubiquitin.


