[gmx-users] how to mimick explicit hydrogen bonding

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 22 00:38:51 CEST 2009

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.


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