1GMX-H2ORDER(1)                      GROMACS                     GMX-H2ORDER(1)
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NAME

6       gmx-h2order - Compute the orientation of water molecules
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SYNOPSIS

9          gmx h2order [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-nm [<.ndx>]]
10                      [-s [<.tpr>]] [-o [<.xvg>]] [-b <time>] [-e <time>]
11                      [-dt <time>] [-[no]w] [-xvg <enum>] [-d <string>]
12                      [-sl <int>]
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DESCRIPTION

15       gmx h2order computes the orientation of water molecules with respect to
16       the normal of the box. The program determines the average cosine of the
17       angle  between  the  dipole moment of water and an axis of the box. The
18       box is divided in slices and  the  average  orientation  per  slice  is
19       printed.   Each  water molecule is assigned to a slice, per time frame,
20       based on the position of the  oxygen.  When  -nm  is  used,  the  angle
21       between  the  water  dipole and the axis from the center of mass to the
22       oxygen is calculated instead of the angle between the dipole and a  box
23       axis.
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OPTIONS

26       Options to specify input files:
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28       -f [<.xtc/.trr/…>] (traj.xtc)
29              Trajectory: xtc trr cpt gro g96 pdb tng
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31       -n [<.ndx>] (index.ndx)
32              Index file
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34       -nm [<.ndx>] (index.ndx) (Optional)
35              Index file
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37       -s [<.tpr>] (topol.tpr)
38              Portable xdr run input file
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40       Options to specify output files:
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42       -o [<.xvg>] (order.xvg)
43              xvgr/xmgr file
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45       Other options:
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47       -b <time> (0)
48              Time of first frame to read from trajectory (default unit ps)
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50       -e <time> (0)
51              Time of last frame to read from trajectory (default unit ps)
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53       -dt <time> (0)
54              Only use frame when t MOD dt = first time (default unit ps)
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56       -[no]w (no)
57              View output .xvg, .xpm, .eps and .pdb files
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59       -xvg <enum> (xmgrace)
60              xvg plot formatting: xmgrace, xmgr, none
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62       -d <string> (Z)
63              Take the normal on the membrane in direction X, Y or Z.
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65       -sl <int> (0)
66              Calculate order parameter as function of boxlength, dividing the
67              box in this number of slices.
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KNOWN ISSUES

70       · The program assigns whole water molecules to a slice,  based  on  the
71         first  atom  of  three  in  the index file group. It assumes an order
72         O,H,H. Name is not important, but the order is. If this demand is not
73         met, assigning molecules to slices is different.
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SEE ALSO

76       gmx(1)
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78       More     information    about    GROMACS    is    available    at    <‐
79       http://www.gromacs.org/>.
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82       2019, GROMACS development team
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872019.2                           Apr 16, 2019                   GMX-H2ORDER(1)
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