[gmx-users] g_rmsf and the -fit option , calculating average structures

[Arneh Babakhani]

I see to calculate the average structure of a protein in a trajectory 
minus any rotational + translational effects, using g_rmsf.   Does the 
-fit option (default yes) eliminate rot + trans contributions? 

Or must one use trjconv first, to convert the trajectory to some 
reference frame eliminating the rot+trans,  and then use g_rmsf on that 
new trajecotry???


Thanks,

Arneh