[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 position restrained 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? The consistent H bonds after 2ns seen due to restraining of
ligand while performing simulation?

Regards,

Adarsh V. K.