[gmx-users] RMSF per residue

[Justin Lemkul]

On 5/26/17 1:20 PM, Mohsen Ramezanpour wrote:
> Hi Justin,
> 
> Here is what I understand. I would like to know if I understood correctly.
> 
> Given a selection, which has all the heavy atoms (5 atoms) in the side
> chain of one specific residue (say Lysine), I want to have only "one value"
> for the average fluctuation of this selection.
> Thus, I will use "-res" option in gmx_rmsf command.
> 
> If I understood correctly, the RMSF for each atom in this selection is
> calculated first. So, we will have the rmsf(i) values, which i=1 to 5.
> Next, a mass-weighted average will be taken over all of these atoms. Thus,
> the final value I get as output is the following:
> 
> RMSF per selection = (Sum (m(i)*rmsf(i)))/(Sum m(i)) where m(i) is the mass
> for atom i.
> 
> Is this correct?
> 
> If yes, why the RMSF per selection should be a mass-weighted?
> In other words, whey the usual average is not used, e.g. (Sum (rmsf(i))/5)
> where 5 is the total number of atoms in this selection.
> 

Because not all atoms have equal contributions to the RMSF value in the first 
place; it's a mass-weighted quantity.  Confirm in the code; it's a rather short 
program.

-Justin

> Thanks
> Mohsen
> 
> On Thu, May 25, 2017 at 12:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
>>
>>
>> On 5/24/17 4:12 PM, Mohsen Ramezanpour wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I have a question on RMSF calculation:
>>>
>>> I am not sure how -res works in RMSF and I could not find any useful
>>> explanation for it.
>>>
>>> It will give the average fluctuations per residue, fine. but how exactly?
>>>
>>> 1) it calculates the RMSF for each atom in that residue first. Then, it
>>> averages over all of these atoms and reports it as the average for the
>>> residue.
>>>
>>> 2) it takes the center of mass or specific atom of the residue and
>>> calculates the RMSF for that.
>>>
>>> Or something else?
>>>
>>>
>>> I am interested in the average fluctuation for sidechain of one residue
>>> (excluding H atoms from this calculation). I want to have only one value
>>> as
>>> the average fluctuation for this group.
>>>
>>> I choose the residue-sidechain-H group (which I made in an index file)
>>> when
>>> prompted in the following command:
>>>
>>> gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
>>>   residues-sidechain-H.xvg  -res
>>>
>>>
>>> an alternative would be to use the following command and make an average
>>> over all atoms manually:
>>>
>>> gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
>>>   residues-sidechain-H.xvg
>>>
>>>
>>> The results are NOT the same as expected. I think I should use the second
>>> command and make the average manually. What do you think?
>>>
>>>
>> The total RMSF of the selection is computed, then a mass-weighted average
>> over each of the atoms is computed and that subsequent value assigned for
>> output. See the "average_residues" function in
>> src/gromacs/gmxana/gmx_rmsf.cpp
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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> 
> 
> 

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================