[gmx-users] least-squares fitting the second structure on the reference structure

[Qasim Pars]

Dear users,

From GROMACS online manual:
gmx confrms computes the root mean square deviation (RMSD) of two structures after least-squares fitting the second structure on the first one. 

My question is how GROMACS does least-squares fitting the second structure (each frame of trajectory) on the first one (reference structure)? It calculates the least-squares fitting of the second structure and the first one seperately? 

Thanks for your helps.