[gmx-users] Question about documentation of -a switch in g_hbond

Andrew DeYoung adeyoung at andrew.cmu.edu
Sun Jun 10 16:36:03 CEST 2012


This might end up being a silly/embarrassing question, and if so, I
apologize.  I feel like I may be making a conceptual mistake, but I'm not

Is it true that a hydrogen bond is of the following form?

Donor---Hydrogen ... Acceptor

Is this the correct order?  I think so.  For example, in my system, I have:

Oxygen---Hydrogen ... Fluorine

In the documentation, the -a option has this description: 

"Cutoff angle (degrees, Acceptor - Donor - Hydrogen)"

Why is the order Acceptor - Donor - Hydrogen (or, equivalently, Hydrogen -
Donor - Acceptor)?  Why isn't "Hydrogen" instead between "Donor" and
"Acceptor"?  Which angle does -a specify?

Thank you! 
Andrew DeYoung
Carnegie Mellon University 

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