[gmx-users] RMSF analysis

Sainitin Donakonda saigro16 at gmail.com
Wed Oct 9 21:29:29 CEST 2013

Hi all,

I recently performed MD simulation of protein - ligand complex..and
analyzed its trajectory using RMSF tool in gromacs.

This analysis revealed particular residue in binding site of protein showed
quite high fluctuation around 0.30 nm but other residues were in range of
0.15 to 0.20

Can any body explain why this particular residue have  high RMSF value in
compared to other residues


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