[gmx-users] RMSF calculation of carbon alpha

[Tsjerk Wassenaar]

Hi Ebert,

Use C-alpha as the group. Yes, it will be used for fitting and calculation
of the RMSF.

Cheers,

Tsjerk
On Oct 5, 2015 22:44, "Ebert Maximilian" <m.ebert at umontreal.ca> wrote:

> Oh infact no thats not the case it is still the RMSF of all atoms in the
> residue. So back to my initial question. How can I calculate the RMSF on
> the Ca of each residue?
>
> Sorry if this caused any confusion.
>
> Max
>
> > On Oct 5, 2015, at 4:36 PM, Ebert Maximilian <m.ebert at umontreal.ca>
> wrote:
> >
> > I think I can answer my own question again. The group you use for root
> mean square calculation is also the RMSF group. If the group has more than
> one atom per residue and I use -res I get the average RMSF of all atoms per
> residue.
> >
> > Hope this is correct.
> >
> > Max
> >
> >> On Oct 5, 2015, at 2:46 PM, Ebert Maximilian <m.ebert at umontreal.ca>
> wrote:
> >>
> >> Hi there,
> >>
> >> I want to calculate ht RMSF of the carbon alpha. First which atoms are
> used if I calculate the RMSF per residue with -res and how can I calculate
> the RMSF of carbon alpha or NH vector etc? Can’t seem to find an input
> except for the group of the alignment for the -fit
> >>
> >> Thank you,
> >>
> >> Max
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