[gmx-users] Help about g_hbond and angle cutoff

Justin A. Lemkul jalemkul at vt.edu
Sat Jan 14 15:03:00 CET 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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