[gmx-users] RMSF per residue

[Justin Lemkul]

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

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