[gmx-users] Help with g_rmsf

[Tsjerk Wassenaar]

Hi Carla,

> 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.

Have you made sure there are no atoms jumping across the boundaries?

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

If you choose chainA-H, you'll get results for that chain. It will be
used for the fit as well as for the analysis.

> 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.

It does reflect the reality of your simulation. Maybe it does not
reflect what you aimed to get.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands