Dear users, g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res
With the option -od the root mean square deviation with respect to the reference structure is calculated. Then, RMSDEV is the RMSD per residue (the root mean square deviation with respect to the reference structure is calculated). and RMSF is the RMSD per residue (the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame). That is, it is the measurement averaged over all atoms in each residue. Now what difference? I am confused. -- Ahmet YILDIRIM
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