[gmx-users] Hbond occupancy reference rate

larif sofiene larifsofiene at gmail.com
Thu Nov 24 03:27:13 CET 2011

After doing a gormacs MD simulation and finding Hydrogen
bonds,applying Justin script give me the Hbonds occupancy rate,then i
have to choose the most representative structure in the simulation and
show some of my interesting hydrogen bonds for publication purpose.
Should i consider a reference Hbond existence percentage from which
bond between two atoms are significantly existent like for example for
a hbond occupancy rate of 10% we can say that this hbond has a good
chance to exist in reality an effectively participate in the protein
phenomena (movement,structure...) and for another hbond occupancy with
0.7% we can safely ignore it because it will not participate in
protein behavior.
Is there such reference value?
thanks for responding.
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