[gmx-users] RMSF calculation of carbon alpha

[Ebert Maximilian]

Like gmx rms the gmx rmsf tool should be extended to align and calculate on different index groups. That would be helpful. Also maybe we could add some information about the -res flag and the behaviour for aligning and calculating the the gmx rmsf help text. How could I suggest that officially?

Max

> On Oct 6, 2015, at 2:36 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
> 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.
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