[gmx-users] RMSF calculation of carbon alpha

[Ebert Maximilian]

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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