1GMX-H2ORDER(1) GROMACS GMX-H2ORDER(1)
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6 gmx-h2order - Compute the orientation of water molecules
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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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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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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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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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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 2020, GROMACS development team
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872019.6 Feb 28, 2020 GMX-H2ORDER(1)