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

Arneh Babakhani ababakha at mccammon.ucsd.edu
Tue Sep 18 02:04:21 CEST 2007


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





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