[gmx-users] RMSF calculation of carbon alpha

[Ebert Maximilian]

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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