On 3/4/13 7:54 AM, mcapar wrote:
Dear GROMACS users,
In gromacs, the default values of the geometrical criterion of H-bond are
0.35 nm and 30 deg for spc water molecules. The acceptor and donor atoms of
H-bond in my system are different than in the water system. Therefore I
think that I should use suitable D-A distance and H-D-A (alpha) angle for my
system in order to calculate the number of H-bond. I obtained the D-A
distance and the A-H-D angle from Cambridge Structural Database (CSD) but I
couldn’t find the H-D-A angle from CSD.
I want to learn how I can obtain the H-D-A (alpha) angle. If you can answer
me, I’ll be so glad.
The default settings do not apply just to SPC; in fact, they come from average
values obtained from crystallographic databases. There are a few threads with
fairly extensive discussions on this topic. Most papers that I see use similar,
if not identical, settings to g_hbond.
-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
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