[gmx-users] g_rms, least square fit
Mark.Abraham at anu.edu.au
Fri Oct 6 01:51:52 CEST 2006
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
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.
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