I want to get a average structure from a pdb file containing multiple models. I used the command below:

gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av

GROMACS Doc states that the ''-av'' option can ''write average structure of each cluster'', but how does it do it. I think there will be atom clash or unphysical residue structure if it is a simple average of atom positions, however, the result above seemed rational.

On the other hand, the GROMACS website also has a suggestion about average structure:

http://www.gromacs.org/Documentation_of_outdated_versions/Terminology/Average_Structure

I am confused by the algorithm, and I wish someone can help me!

Thank you!