[gmx-users] G_rmsf, reference structure

[Eerden, van, F.J.]

Dears,

I have calculated the RMSF from a protein trajectory in Gromacs 4.5.5.

My question is how the RMSF is calculated:
A)
1) fitting of the trajectory to the tpr file supplied by -s
2) calculating the averaged atom coordinates over time (x~)
3) calculating the deviation from the averaged structure (x-x~), for each
time frame
4) averaging over all time frames <x-x~>

OR
B)
1) fitting of the trajectory to the tpr file supplied by -s
2) calculating the deviation from the TPR structure (x-x*), for each time
frame
3) averaging over all time frames <x-x*>

This question has already popped up multiple times in the mailing list:
https://www.mail-archive.com/gmx-users@gromacs.org/msg25391.html
and
http://comments.gmane.org/gmane.science.biology.gromacs.user/38359

The problem is that there are multiple answers given:
In the first one, it is argued that method A is used
in the second mailing list, Marc Abraham states that method B is being
used, while Tsjerk mentions method A.

I tried to resolve this by looking into thee source code,
and although to me it seems that it is option, B, I do not trust my Gromacs
code reading capabilities that well ;)

Happy Easter!

Floris