[gmx-users] How to interpret gmx H_bond analysis?

[Adarsh V. K.]

Dear gmx users,

How to interpret gmx H_bond analysis?

I have done 20 ns simulation of a protein-ligand complex
(Enzyme-inhibitor). The H-bond analysis shows absence of H-bonds (zero) in
several frames during the first 2ns of simulation. But from 2 ns onwards
consistent (at least one) H bonds are seen till the end of simulation (Is
this due to restraining of ligand?)

How can we interpret this protein-ligand simulation.

Whether the ligand will 'fall off' from the protein during the first 2 ns
of simulation since there are many zero H bonds till reaching 2 ns?
Why consistent H bonds after 2ns seen ?

Regards,

Adarsh V. K.