ms wrote:
Hi Mark,
Thanks for your answer.
Mark Abraham ha scritto:
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).
Ok, the problem is that I want to re-implement a quite minimal
coarse-grained FF (so no explicit solvent etc.) and a directional
interaction would be useful.
Well you should consider alternative software, then.
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.
I see. I asked because I think I've read that there were force fields
with explicit hydrogen bond treatment (some CHARMM?) that were imported
into Gromacs, and I thought there was some clever hack to get it working
-but I guess that it is not the case.
IIRC, CHARMM did have explicit H-bond models ages ago, but (again IIRC)
they're not in the modern versions and not in the upcoming GROMACS port.
Mark
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