ms wrote:
Hi,
I need to implement a FF which includes directional hydrogen bonding. It
seems however, to my understanding, that Gromacs has no simple way to
include an explicitly directional contribution. All I can find is that,
in standard force fields, h-bond terms are implicitly described by
coulombic and vdw interactions, but I am a bit puzzled by how these
terms are combined to give a directional interaction.
There's nothing directional about the physics of a hydrogen bond, unless
your model makes it so. There'd be nothing intrinsically valid or
invalid with that either, so long as you parameterized the force field
under that assumption. If using rigid water models and/or other atomic
constraints where H-bonded atoms can't have a geometric distortion, I
suppose such a model might be necessary. It's still far from clear that
H-bonding is sufficiently different from other electrostatic
interactions to warrant special treatment (and thus reparameterization
of charges).
Can anyone give me hints on how to describe a directional
hydrogen-bond-like interaction?
You would not achieve this in GROMACS without code modification. A
special non-bonded list for H-bonded water (and maybe H-bonded
non-water) that didn't call the standard water inner loops would be
required.
MArk
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