[gmx-users] hbond definition in simulations

[Justin Lemkul]

On 7/19/16 10:07 AM, Joel Markgren wrote:
> 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.
>

There is no explicit hydrogen bonding term.  GROMACS does nothing special; these 
interactions are governed almost entirely by the electrostatic terms (partial 
charges) in the force field.

-Justin

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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