[gmx-users] g_h2order for 5 sites water

[Mikhail Stukan]

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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