[gmx-users] g_rms, least square fit

[Mark Abraham]

kanin wichapong wrote:
> Dear All,
>        I have some questions about g_rms. When I start to calculate the 
> rmsd using g_rms first I will get "Select group for least squares fit" 
> and then "Select group for RMSD calculation", does both two times need 
> to be the same group or not? 

You can fit based on one group of atoms, and then compare the fit based 
on another group of atoms.

> Like in my case, I want to calculate rmsd 
> of one residue of the inhibitor which is tetrapeptide. What should be 
> selected for the least square fit, Backbone of protein, all residue of 
> inhibitor group or the group of the residue that I want to calculate the 
> rmsd?

Pick something you think should make a constant reference frame and use 
that for the fitting. Then use the group you think should vary for the 
RMSD calculation. Or just play with it and see.

Mark