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Hi,<br>
<br>
That suggets it's related to the new merge-on-the-fly-code and not
the pbc handling.<br>
<br>
And it's me, not Justin, who's fixing and probably creating the
bugs. :-)<br>
<br>
Cheers,<br>
<br>
Erik<br>
<br>
Zuzana Benkova skrev 2011-02-16 19.58:
<blockquote cite="mid:fb8f45c2d64.4d5c2c62@savba.sk" type="cite">
<div style="font-family: 'Times New Roman'; font-size: 16px;">Dear
Justin, <br>
<br>
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>
<br>
Greetings<br>
Zuzana<br>
<br>
<span>On 02/15/11, <b class="name">Zuzana Benkova </b>
<a class="moz-txt-link-rfc2396E" href="mailto:Zuzana.Benkova@savba.sk"><Zuzana.Benkova@savba.sk></a> 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>
<a class="moz-txt-link-rfc2396E" href="mailto:erikm@xray.bmc.uu.se"><erikm@xray.bmc.uu.se></a> 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 moz-do-not-send="true"
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 moz-do-not-send="true"
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>
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</blockquote>
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</blockquote>
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</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
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
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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