Dear gromacs users,
I have run a MD of 2 short peptides respectively, I want to compare the
flexibility between these two peptides along the full sequence via the
per-residue RMSF.
I understand that gmx rmsf computes the root mean square fluctuation of atomic
positions in the trajectory (supplied with -f) after(optionally) fitting to a
reference frame (supplied with -s), namely using "fit" option. Well, I am
confused that if we add "nofit" option when calculating RMSF, does gmx rmsf
still fit before computing rms flucuation? If so, what structure does gmx rmsf
fit to since no fitting to reference structure(supplied with -s)?
Best regards,
Ouyang
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