[gmx-users] How to get angle distribution between two tyrosine stacking residues

[chris.neale at utoronto.ca]

1. Determine some mathematical calculation that you want to apply to  
some atoms.
2. make a .ndx group that includes all of those atoms
3. Run g_traj -ox to output the coordinates of those atoms
4. Apply your mathematical calculation using awk.

-- original message --

Can anyone tell how to calculate the normal-normal angle between two
stacking tyrosine residues as a function of time.