alejandro esteban blanco munoz wrote:
Hi gromacs Users:
I have a doubt respect to how g_hbond consider the cutoff angle (-a)
Acceptor-Donnor-Hydrogen in gromacs 4.5.4. I need to evaluate the
hydrogen bonds with an anble larger than 135°. The default value of the
angle is cutoff in g_hbond is 30°, so this value means that the H. bonds
larger than 30° will be evaluated? or the angles to evaluate will be
larger than 150° (180° - 30°) as is proposed in this post for gromacs
3.1.1: http://lists.gromacs.org/pipermail/gmx-users/2003-January/003970.html
If the second case was correct, then the value to use in my case should
be "-a 45" for looking all H. bonds larger than 135°?
Yes, note the order of the terms. The default value of 30 degrees corresponds
to the A-D-H angle, so that would make the D-H-A value (which is I think what
you are considering) 150 degrees in the default case.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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