Greetings,
I want to compute time dependent variations in area between four residues (forming a bottle neck for ligand entry). I was looking at pairdist and dist tools of gromacs but i couldnot conclude which one can i use for my analysis.
A____B
|++++ |
C____D
lets say i have to calculate changes in the area between theses four residue. should i make index for four single residues or in pairs, to calculate dist and area eventually?