[gmx-users] Help with g_rmsf

[Carla Jamous]

Hi everyone,

please I have a litle problem:

during my simulation, the dimer I'm simulating changed a lot.
So when I calculate with g_rms, the RMSD between my initial and my final
structure (choosing "Protein-H"), I get a value of 10 angstroms.

However, when I try to calculate a RMSDeviation averaged over residue using
g_rmsf -od , between the first chain of the initial and final structure, I
get RMSDeviation per residue values that don't exceed 3 or 4 angstroms.

Please can anyone explain how g_rmsf works?
If I do the following:

g_rmsf -s initial.pdb -f final.pdb -od rmsdev.xvg -res (I choose
"chainA-H"),

does g_rmsf fit one the whole dimer and then calculate rmsdeviation of
chainA or does it fit on chainA and then calculate RMSdeviation of chainA.
In the latter case, my result does not reflect the reality of my simulation.

Please if anyone knows the answer, I would really appreciate some help.

Thanks,
Carla
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