[gmx-users] g_hbond and 4.5.2 version

[Erik Marklund]

Hi,

That suggets it's related to the new merge-on-the-fly-code and not the 
pbc handling.

And it's me, not Justin, who's fixing and probably creating the bugs. :-)

Cheers,

Erik

Zuzana Benkova skrev 2011-02-16 19.58:
> Dear Justin,
>
> maybe following information helps you. When I evaluated the number of 
> hydrogen bonds between two different groups, particularly, water and 
> frozen atoms of the siloxane surface I got the same results with both 
> version of GROMACS, 4.0.3 and 4.5.2.
>
> Greetings
> Zuzana
>
> On 02/15/11, *Zuzana Benkova * <Zuzana.Benkova at savba.sk> wrote:
>> Hello Justin,
>>
>> I was using cubic boxes.
>>
>> Greetings
>> Zuzana
>>
>> On 02/15/11, *Erik Marklund * <erikm at xray.bmc.uu.se> wrote:
>>> 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/
>>>
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-- 
-----------------------------------------------
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/

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