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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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