On 6/10/12 10:36 AM, Andrew DeYoung wrote:
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?
Because it's easy to define from an algorithmic standpoint. A hydrogen bond is
stronger depending on how close to linearity it is. Measuring an acute angle
given by -a says that if the A-D-H angle is less than 35 degrees, you can vary
between 0 and 35 easily to show the same thing as being within a certain range
of being 180 degrees in terms of D-H-A.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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
