Hello Justin,
I was using cubic boxes.
Greetings
Zuzana
On 02/15/11, Erik Marklund <er...@xray.bmc.uu.se> wrote:
I was using cubic boxes.
Greetings
Zuzana
On 02/15/11, Erik Marklund <er...@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
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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