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

[Peter C. Lai]

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.

-- 
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Peter C. Lai			| University of Alabama-Birmingham
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pcl at uab.edu			| Birmingham AL 35294-4461
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