[gmx-users] Hydrogen bonds with version 3.3.1

[David van der Spoel]

Gianluca Interlandi wrote:
>>>>The hbond program is rather complex, but the hbond criterion itself is not
>>>>(but note that the definition of the angle has changed from 3.2.1 to 3.3,
>>>>from
>>>>AHD to ADH).
>>>
>>>This hasn't been clear to me as the online documentation says DHA:
>>>
>>>-a  real  30  Cutoff angle (degrees, Donor - Hydrogen - Acceptor)
>>
>>in that case you're running an old version of gromacs. Try
>>which g_hbond
> 
> 
> I'm using version 3.3.1 (gromacs-3.3.1-1.i386.rpm). I was refering to the 
> online documentation:
> 
> http://www.gromacs.org/documentation/reference_3.3/online/g_hbond.html

I see, that documentation is apparently outdated. Please use g_hbond -h 
for more up to date info.
But now for the most important question: is there a reproducible problem 
with the angle?

> 
> Gianluca
> 
> -----------------------------------------------------
> Dr. Gianluca Interlandi gianluca at u.washington.edu
>                     +1 (206) 685 4432
>                     +1 (206) 714 4303
>                     http://biocroma.unizh.ch/gianluca/
> 
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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