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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Dear gmx-users,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I have the following problem with g_h2order tool (4.0.7 and
4.5.1 versions). It works perfectly fine when I apply it to a box of SPC/E
water, but I have something really strange if I try to apply it to SW or
SWM4-NDP water models (both are 5 sited models). In my index file I have a group
which looks like <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>[ Water ]<o:p></o:p></p>
<p class=MsoNormal>1 2 3 6 7 8 11 12 13
….<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>All shell particles (numbers 5,10 etc) and virtual sites (numbers
4, 9, etc) are omitted, O,H,H order is correct. But the results I receive are obviously
wrong. I have order.xvg file which looks like. What is the most strange is that
the output is independent on –d option. What am I doing wrong?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal># This file was created Tue Oct 5 15:41:30 2010<o:p></o:p></p>
<p class=MsoNormal># by the following command:<o:p></o:p></p>
<p class=MsoNormal># g_h2order4.5.1 -f sw4.gro -n index.ndx -s sw4.tpr -d Z<o:p></o:p></p>
<p class=MsoNormal>#<o:p></o:p></p>
<p class=MsoNormal># g_h2order4.5.1 is part of G R O M A C S:<o:p></o:p></p>
<p class=MsoNormal>#<o:p></o:p></p>
<p class=MsoNormal># Grunge ROck MAChoS<o:p></o:p></p>
<p class=MsoNormal>#<o:p></o:p></p>
<p class=MsoNormal>@ title "Water orientation with
respect to normal"<o:p></o:p></p>
<p class=MsoNormal>@ xaxis label "box (nm)"<o:p></o:p></p>
<p class=MsoNormal>@ yaxis label "mu_x, mu_y, mu_z
(D), cosine with normal"<o:p></o:p></p>
<p class=MsoNormal>@TYPE xy<o:p></o:p></p>
<p class=MsoNormal> 0.000 208.441
234.923 6.737 2.596742e-02<o:p></o:p></p>
<p class=MsoNormal> 0.101 218.501 194.438
22.236 7.899551e-02<o:p></o:p></p>
<p class=MsoNormal> 0.201 242.260 197.469
33.994 1.243817e-01<o:p></o:p></p>
<p class=MsoNormal> 0.302 155.735 211.908
46.930 2.177687e-01<o:p></o:p></p>
<p class=MsoNormal> 0.402 248.467 214.602
60.764 1.884665e-01<o:p></o:p></p>
<p class=MsoNormal> 0.503 203.367 224.841
75.197 2.791217e-01<o:p></o:p></p>
<p class=MsoNormal> 0.603 225.723 207.376
88.851 2.910973e-01<o:p></o:p></p>
<p class=MsoNormal> 0.704 214.146 223.984 103.027
3.272970e-01<o:p></o:p></p>
<p class=MsoNormal> 0.805 233.803 187.219 116.877
3.938356e-01<o:p></o:p></p>
<p class=MsoNormal> 0.905 199.563 245.420 129.262
3.936486e-01<o:p></o:p></p>
<p class=MsoNormal> 1.006 188.535 196.094 143.064
4.543617e-01<o:p></o:p></p>
<p class=MsoNormal> 1.106 212.706 249.064 156.556
4.418467e-01<o:p></o:p></p>
<p class=MsoNormal> 1.207 211.675 205.420 171.057
5.094404e-01<o:p></o:p></p>
<p class=MsoNormal> 1.308 246.957 186.864 185.596
5.123689e-01<o:p></o:p></p>
<p class=MsoNormal> 1.408 207.272 226.950 197.887
5.508973e-01<o:p></o:p></p>
<p class=MsoNormal> 1.509 221.945 185.566 211.389
5.808831e-01<o:p></o:p></p>
<p class=MsoNormal> 1.609 224.529 218.854 227.235
5.853382e-01<o:p></o:p></p>
<p class=MsoNormal> 1.710 196.245 182.504 238.778
6.468648e-01<o:p></o:p></p>
<p class=MsoNormal> 1.810 228.958 253.420 253.580
5.898822e-01<o:p></o:p></p>
<p class=MsoNormal> 1.911 186.654 181.046 267.176
6.963417e-01<o:p></o:p></p>
<p class=MsoNormal> 2.012 220.318 225.659 278.641
6.373896e-01<o:p></o:p></p>
<p class=MsoNormal> 2.112 209.207 205.927 294.242
6.980361e-01<o:p></o:p></p>
<p class=MsoNormal> 2.213 223.278 232.911 308.723
6.743686e-01<o:p></o:p></p>
<p class=MsoNormal> 2.313 189.832 194.477 320.685
7.507596e-01<o:p></o:p></p>
<p class=MsoNormal> 2.414 210.459 248.153 335.703
6.921831e-01<o:p></o:p></p>
<p class=MsoNormal> 2.514 223.793 207.197 348.529
7.283705e-01<o:p></o:p></p>
<p class=MsoNormal> 2.615 198.909 185.450 362.836
7.815984e-01<o:p></o:p></p>
<p class=MsoNormal> 2.716 171.940 219.477 376.684
7.800925e-01<o:p></o:p></p>
<p class=MsoNormal> 2.816 236.925 218.644 388.275
7.497334e-01<o:p></o:p></p>
<p class=MsoNormal> 2.917 240.590 199.067 403.015
7.664154e-01<o:p></o:p></p>
<p class=MsoNormal> 3.017 177.790 196.700 416.747
8.174569e-01<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thank you very much in advance,<o:p></o:p></p>
<p class=MsoNormal>Mikhail<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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