[gmx-users] Hydrogen bonding criteria in Gromacs

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
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