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
[email protected] http://folding.bmc.uu.se/
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
