[gmx-users] RMSF per residue

[Mohsen Ramezanpour]

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.

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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
*Rewards work better than punishment ...*