[gmx-users] Different sets of residues for ensemble fitting and RMSF calculation

[Mark Berjanskii]

Dear all, 

Is it possible to use different sets of residues for alignment of a
protein ensemble and for calculation of RMSF?

I am trying to get a plot RMSF vs residue number from a Gromacs 
trajectory. I have an extended very flexible region in a protein of
interest that I do not want to use for ensemble alignment because it
will make RMSF of rigid secondary structure elements unreasonably big.


Unfortunately, g_rmsf uses the same atom/residue selection for both
ensemble alignment and calculation of RMSF. 

 Is it possible to somehow use only secondary structure regions of a
protein for ensemble alignment but, then, calculate RMSF for each
residue of the protein?

Thank you, 


Mark