[gmx-users] Hydrogen bonding criteria in Gromacs

[Justin Lemkul]

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

==================================================