[gmx-users] Question about documentation of -a switch in g_hbond
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?
Carnegie Mellon University
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