[gmx-users] RMSF calculation of carbon alpha

[Tsjerk Wassenaar]

Right :)

Cheers,

Tsjerk

On Mon, Oct 5, 2015 at 11:07 PM, Ebert Maximilian <m.ebert at umontreal.ca>
wrote:

> Thanks for the clarification Tsjerk. So my previous assumption was right.
> Basically if I want to align on the backbone but want the RMSF of Calpha I
> need to align first, save the trajectory and do RMSF with -nofit right?
>
> Max
>
> > On Oct 5, 2015, at 4:54 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> >
> > 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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-- 
Tsjerk A. Wassenaar, Ph.D.