[gmx-users] g_hbond and 4.5.2 version

[Erik Marklund]

Justin A. Lemkul skrev 2011-02-09 23.03:
>
>
> 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
>>
>
Are people who are reporting this error using a triclinic boxes or 
cuboid boxes. That information may help my bugfixing.

-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/