[gmx-users] Interpretation of RMSD matrix

[Apramita Chand]

Dear All,
I would be grateful if you could help me with links to relevant
papers/websites/sources on how to interpret RMSD matrices when comparing
all frames of   single trajectory to reference structure and also when
comparing two different trajectories.

I am taking the reference structure from the input .tpr file. What in your
opinion, is a better option to compare when taking RMSD? The starting
structure .gro file or the .tpr file(after equilibration) ?


Yours sincerely
Apramita