[gmx-users] hbond definition in simulations

[Joel Markgren]

Dear GROMACS users,

I have understood that GROMACS has following definition on hydrogen bonds: is a geometric definition, and it states that for a hydrogen bond to be present the donor-hydrogen· · ·acceptor angle is no greater than 30 ◦ and the oxygen-oxygen cut-off distance at most 0.35 nm.

But what is the definition, of the bond itself? What I have learned does hydrogen bonds involve stronger forces then regular electrostatics, how does GROMACS formulate the forces involved in hydrogen bonding’s within an simulation. I somehow take it naturally that md simulations do take into account hydrogen bond formations.

Best regards and many thanks for response

Joel Markgren
PhD student in Biology

Sveriges lantbruksuniversitet
Swedish University of Agricultural Sciences

Department of Plant Breeding
PO Box 101, Sweden 23053 Lund
Visiting address: Sundsvägen 10, 23053 Lund
Mobile: +46 706101128
joel.markgren at slu.se, www.slu.se<http://www.slu.se/>
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