<div style="font-family: 'Times New Roman'; font-size: 16px;">Dear Justin, <br _moz_dirty="" /><br _moz_dirty="" />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.<br _moz_dirty="" /><br _moz_dirty="" />Greetings<br _moz_dirty="" />Zuzana<br /><br /><span>On 02/15/11, <b class="name">Zuzana Benkova </b> <Zuzana.Benkova@savba.sk> wrote:</span><blockquote cite="mid:fbb9328a580b.4d5a8576@savba.sk" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div style="font-family: 'Times New Roman'; font-size: 16px;">Hello Justin, <br /><br />I was using cubic boxes. <br /><br />Greetings<br />Zuzana<br /><br /><span>On 02/15/11, <b class="name">Erik Marklund </b> <erikm@xray.bmc.uu.se> wrote:</span><blockquote cite="mid:4D5A5969.5020703@xray.bmc.uu.se" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text plain">Justin A. Lemkul skrev 2011-02-09 23.03:<br />><br />><br />>Zuzana Benkova wrote:<br />>>Dear GROMACS users,<br />>><br />>>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.<br />>>However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2.<br />>>I would appreciate any help. Thank you in advance.<br />>><br />><br />>Try pulling the latest stable development version. This issue was reported in 4.5.1:<br />><br />><a href="http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html</a><br />><br />>but not fixed until after 4.5.3 was released:<br />><br />><a href="http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html</a><br />><br />>-Justin<br />><br />>>Greetings<br />>>Zuzana<br />>><br />><br />Are people who are reporting this error using a triclinic boxes or cuboid boxes. That information may help my bugfixing.<br /><br />-- <br />-----------------------------------------------<br />Erik Marklund, PhD student<br />Dept. of Cell and Molecular Biology, Uppsala University.<br />Husargatan 3, Box 596, 75124 Uppsala, Sweden<br />phone: +46 18 471 4537 fax: +46 18 511 755<br />erikm@xray.bmc.uu.se <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a><br /><br />-- <br />gmx-users mailing list gmx-users@gromacs.org<br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br />Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br />Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@gromacs.org.<br />Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br /></div></blockquote></div>
</div></blockquote></div>