[gmx-users] g_hbond and 4.5.2 version

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 9 23:03:24 CET 2011

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 


but not fixed until after 4.5.3 was released:



> Greetings
> Zuzana


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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