[gmx-users] Hydrogen bonding criteria in Gromacs

[Myunggi Yi]

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?


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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>