[gmx-users] G_rmsf, reference structure

[Tsjerk Wassenaar]

Hi Floris,

By default it's A. There is an option for doing B. But B makes no sense.

Cheers,

Tsjerk
On Apr 3, 2015 1:10 PM, "Eerden, van, F.J." <f.j.van.eerden at rug.nl> wrote:

> 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
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