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

[Mark Abraham]

Arneh Babakhani wrote:
> 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?

Yes, it will. If it can't rotate and translate, it's not much of a fit :-)

> 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???

You could try it and see?

Mark