[gmx-users] RMSF per residue

[Mohsen Ramezanpour]

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?

Cheers
Mohsen

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