Dear gmx-users, 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
[ Water ] 1 2 3 6 7 8 11 12 13 .... 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? # This file was created Tue Oct 5 15:41:30 2010 # by the following command: # g_h2order4.5.1 -f sw4.gro -n index.ndx -s sw4.tpr -d Z # # g_h2order4.5.1 is part of G R O M A C S: # # Grunge ROck MAChoS # @ title "Water orientation with respect to normal" @ xaxis label "box (nm)" @ yaxis label "mu_x, mu_y, mu_z (D), cosine with normal" @TYPE xy 0.000 208.441 234.923 6.737 2.596742e-02 0.101 218.501 194.438 22.236 7.899551e-02 0.201 242.260 197.469 33.994 1.243817e-01 0.302 155.735 211.908 46.930 2.177687e-01 0.402 248.467 214.602 60.764 1.884665e-01 0.503 203.367 224.841 75.197 2.791217e-01 0.603 225.723 207.376 88.851 2.910973e-01 0.704 214.146 223.984 103.027 3.272970e-01 0.805 233.803 187.219 116.877 3.938356e-01 0.905 199.563 245.420 129.262 3.936486e-01 1.006 188.535 196.094 143.064 4.543617e-01 1.106 212.706 249.064 156.556 4.418467e-01 1.207 211.675 205.420 171.057 5.094404e-01 1.308 246.957 186.864 185.596 5.123689e-01 1.408 207.272 226.950 197.887 5.508973e-01 1.509 221.945 185.566 211.389 5.808831e-01 1.609 224.529 218.854 227.235 5.853382e-01 1.710 196.245 182.504 238.778 6.468648e-01 1.810 228.958 253.420 253.580 5.898822e-01 1.911 186.654 181.046 267.176 6.963417e-01 2.012 220.318 225.659 278.641 6.373896e-01 2.112 209.207 205.927 294.242 6.980361e-01 2.213 223.278 232.911 308.723 6.743686e-01 2.313 189.832 194.477 320.685 7.507596e-01 2.414 210.459 248.153 335.703 6.921831e-01 2.514 223.793 207.197 348.529 7.283705e-01 2.615 198.909 185.450 362.836 7.815984e-01 2.716 171.940 219.477 376.684 7.800925e-01 2.816 236.925 218.644 388.275 7.497334e-01 2.917 240.590 199.067 403.015 7.664154e-01 3.017 177.790 196.700 416.747 8.174569e-01 Thank you very much in advance, Mikhail
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