[gmx-users] g_rms/rmsf: fit vs. nofit

[Justin Lemkul]

On 11/2/12 7:11 PM, Peter C. Lai wrote:
> Hi
>
> I have sort of a noob question about when to fit and when not to fit when
> computing rmsd and rmsf.
>
> My use-case is to look at the motion of different domains of a protein
> where there are atoms near the COM of the starting structure that remain
> relatively stable throughout the simulation according to g_traj.
>
> Right now, I have been using trjconv -center the trajectory on this core alpha
> carbon then using trjconv -dump and grompp to generate a recentered starting
> structure .tpr. Then I am running g_rms or g_rmsf -nofit against the recentered
> .tpr as the reference.
>
> Is this wildly inappropriate? Should I be fitting against an index group
> consisting of that atom instead? Because the backbone is supposed to be
> shifting I want to minimize any artifacts that would potentially dampen an
> observable residue motion just because the rmsd was computed after a fit,
> and centering the trajectory on an atom near the starting COM would minimize
> distances traveled due to COM diffusion through the solvent.
>

Centering on a single atom can give you spurious results - you'll get false 
contributions from global rotation.  You also can't fit to a single atom, so you 
need a group to which to fit.  If you're looking at motions of one domain 
relative to another, you could fit to one domain and measure relative to it, 
since then the other domain is free to move with respect to the fitted domain.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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