[gmx-users] g_hbond and 4.5.2 version

[Justin A. Lemkul]

Zuzana Benkova wrote:
> Dear GROMACS users,
> 
> I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds 
> in water. I got the average  number per time frame and number of water 
> oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 
> 1.677, which is twice the former value. TIP3P model predicts over 3 
> hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply 
> the digit from version 4.0.7. by 2 I get the expected number. That is 
> why I supposed that the number of 1.677 means per one water oxygen and  
> per one water molecule means 2x1.677 since two water molecules 
> participate at one hydrogen bond.
> However, I do not know yet if my interpretation is correct and how to 
> interpret the number obtained by version 4.5.2.
> I would appreciate any help. Thank you in advance.
> 

Try pulling the latest stable development version.  This issue was reported in 
4.5.1:

http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html

but not fixed until after 4.5.3 was released:

http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html

-Justin

> Greetings
> Zuzana
> 

-- 
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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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