[gmx-users] how to mimick explicit hydrogen bonding

ms devicerandom at gmail.com
Wed Oct 21 13:54:04 CEST 2009

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.

>> 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.


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