[gmx-users] Do hydrogen bonds innately exist using mdrun?

Justin Lemkul jalemkul at vt.edu
Mon Feb 11 21:14:02 CET 2019

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On 2/10/19 1:48 PM, James wrote:
> Hi Justin,
> Thank you for the information. This is a bit disheartening:
> "There is no water model that achieves correct agreement with all
> structural, dynamic, and thermodynamic properties of water"
> But, I guess that's what you get with force fields rather than using QM
> methods. If you have any familiarity with them, do you think any of the
> reactive force fields are better? (Though even if they are I gather they
> are about 50X slower, which is essentially intractable for many models)

A reactive model only makes sense if you care about proton transfer. I 
don't use such models but would not believe that they're magically 
better than any existing non-reactive, additive model. The problem with 
any classical force field is a combination of failure to account for 
charge/proton transfer and polarization (we've made progress on the 
latter, and though they are better, even polarizable models are not 



Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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