Greetings, 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 sure.
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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
