[gmx-users] Hydrogen bonding criteria in Gromacs

[Myunggi Yi]

Dear users,

If H-D-A angle is 30 degrees (for a case D-H distance is 1.0 A and D-A
distance is 3.3 A)
then the angle D-H-A is 138.3915 degrees.

D-A distance: 3.3 Angstroms and H-D-A angle: 30 degrees
are generous criteria to identify most hydrogen bonds.

It seems many people use them too.



On Thu, Jan 16, 2020 at 8:20 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/15/20 10:05 PM, Myunggi Yi wrote:
> > Dear Dr. Justin Lemkul,
> >
> > Can you explain why the D-H-A is 150?
> >
> > If H-D-A is 30, then D-H-A should be smaller than 150 degrees.
> > Since the sum of interior angles of a triangle should be 180 degrees...
> > See the following triangle.
> >
> >                       H
> >
> > D                                                           A
> >
> >
> > Am I missing something?
> >
>
> It's a deviation from linearity. An ideal hydrogen bond has a D-H-A
> angle of 180, thus H-D-A of 0. So the 30 degree values specified in
> GROMACS is effectively the deviation from linearity rather than being
> the complement of this value, which other software uses.
>
> -Justin
>
> > On Thu, Jan 16, 2020 at 2:30 AM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 1/15/20 11:57 AM, Pandya, Akash wrote:
> >>> Hi all,
> >>>
> >>> I  wanted to ask a couple of questions about the hydrogen bonding
> >> calculation in Gromacs.
> >>>
> >>>     1.   Why is the default angle cutoff 30 degrees? The reason I ask
> >> this is because I’ve seen in other packages with higher angle cutoffs.
> >>
> >> It depends on how the software defines the angle. The GROMACS convention
> >> is the angle corresponds to H-D-A rather than D-H-A like some other
> >> programs. H-D-A cutoff of 30 degrees is equivalent to the "conventional"
> >> 150-degree D-H-A cutoff.
> >>
> >>>     2.  What’s the best way to define cutoffs for my system? I know
> this
> >> is ambiguous, but is there a procedure I can use to decide?
> >>
> >> The default criteria are widely used and usually don't require any
> tuning.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
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