[gmx-users] Hydrogen bonds with version 3.3.1

Gianluca Interlandi gianluca at u.washington.edu
Tue May 2 00:49:00 CEST 2006

Dear gmx-users,

I am trying to calculate hydrogen bonds with gromacs version 3.3.1 I would 
like to have a cutoff of 2.7 A between hydrogen and acceptor and an angle 
cutoff of 60 degrees. For that I'm using the following command:

g_hbond -f simulation.trr -s topol.tpr -r 0.27 -a 60 -noda -nonitacc -hbm 
-hbn -nomerge

It seems that the cutoff "-a 60" is used on the angle 
Donor-Hydrogen-Acceptor instead of Hydrogen-Donor-Acceptor. As a result it 
selects hydrogen bonds which are extremely bent and disregards hydrogen 
bonds which are almost planar. This is exaclty the contrary of what it 
should do. Does anyone have experience in calculating hydrogen bonds with 
version 3.3.1?

Thanks a lot,


Dr. Gianluca Interlandi gianluca at u.washington.edu
                    +1 (206) 685 4432
                    +1 (206) 714 4303

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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