[gmx-users] RMSD question

[ingram]

Dear GROMACS community,

I am trying to identify the number of unique peptide structures on the 
surface of a slab. If I simply calculate the RMSD between the protein 
atoms in each frame of the trajectory this tells me nothing about how 
these structures compare on the surface as the constraint of the surface 
will not be taken into account. Can anyone suggest what I should use as 
a reference structure and what I structures I should compare when 
calculating the RMSD


BEst

Teresa