[gmx-users] g_hbond and 4.5.2 version
erikm at xray.bmc.uu.se
Tue Feb 15 11:46:01 CET 2011
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:
> but not fixed until after 4.5.3 was released:
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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