1g_h2order(1)              GROMACS suite, VERSION 4.5              g_h2order(1)
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NAME

6       g_h2order - computes the orientation of water molecules
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8       VERSION 4.5
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SYNOPSIS

11       g_h2order  -f  traj.xtc  -n  index.ndx  -nm  index.ndx  -s topol.tpr -o
12       order.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w
13       -xvg enum -d string -sl int
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DESCRIPTION

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

26       -f traj.xtc Input
27        Trajectory: xtc trr trj gro g96 pdb cpt
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29       -n index.ndx Input
30        Index file
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32       -nm index.ndx Input, Opt.
33        Index file
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35       -s topol.tpr Input
36        Run input file: tpr tpb tpa
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38       -o order.xvg Output
39        xvgr/xmgr file
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OTHER OPTIONS

43       -[no]hno
44        Print help info and quit
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46       -[no]versionno
47        Print version info and quit
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49       -nice int 19
50        Set the nicelevel
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52       -b time 0
53        First frame (ps) to read from trajectory
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55       -e time 0
56        Last frame (ps) to read from trajectory
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58       -dt time 0
59        Only use frame when t MOD dt = first time (ps)
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61       -[no]wno
62        View output xvg, xpm, eps and pdb files
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64       -xvg enum xmgrace
65        xvg plot formatting:  xmgrace,  xmgr or  none
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67       -d string Z
68        Take the normal on the membrane in direction X, Y or Z.
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70       -sl int 0
71        Calculate order parameter as function of boxlength, dividing  the  box
72       in nr slices.
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KNOWN PROBLEMS

76       -  The  program  assigns whole water molecules to a slice, based on the
77       firstatom of three in  the  index  file  group.  It  assumes  an  order
78       O,H,H.Name  is  not  important, but the order is. If this demand is not
79       met,assigning molecules to slices is different.
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SEE ALSO

83       gromacs(7)
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85       More  information  about  GROMACS  is  available  at   <http://www.gro‐
86       macs.org/>.
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90                                Thu 26 Aug 2010                   g_h2order(1)