[gmx-users] RMSF per residue

[Mohsen Ramezanpour]

Thanks Justin!

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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