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

6       g_sorient - analyzes solvent orientation around solutes
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8       VERSION 4.5
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SYNOPSIS

11       g_sorient  -f  traj.xtc  -s  topol.tpr  -n  index.ndx  -o  sori.xvg -no
12       snor.xvg -ro sord.xvg -co scum.xvg -rc scount.xvg  -[no]h  -[no]version
13       -nice  int  -b time -e time -dt time -[no]w -xvg enum -[no]com -[no]v23
14       -rmin real -rmax real -cbin real -rbin real -[no]pbc
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DESCRIPTION

17       g_sorient analyzes solvent orientation around solutes.   It  calculates
18       two  angles  between the vector from one or more reference positions to
19       the first atom of each solvent molecule:
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21       theta1: the angle with the vector from the first atom  of  the  solvent
22       molecule to the midpoint between atoms 2 and 3.
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24       theta2:  the angle with the normal of the solvent plane, defined by the
25       same three atoms, or when the option  -v23 is set the  angle  with  the
26       vector between atoms 2 and 3.
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28       The  reference  can be a set of atoms or the center of mass of a set of
29       atoms. The group of solvent atoms should consist of 3 atoms per solvent
30       molecule.  Only solvent molecules between  -rmin and  -rmax are consid‐
31       ered for  -o and  -no each frame.
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34        -o: distribtion of cos(theta1) for rmin=r=rmax.
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37        -no: distribution of cos(theta2) for rmin=r=rmax.
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40        -ro: cos(theta1) and 3cos2(theta2)-1 as a function of the distance.
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43        -co:  the  sum  over  all  solvent  molecules  within  distance  r  of
44       cos(theta1) and 3cos2(theta2)-1 as a function of r.
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47        -rc: the distribution of the solvent molecules as a function of r
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FILES

50       -f traj.xtc Input
51        Trajectory: xtc trr trj gro g96 pdb cpt
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53       -s topol.tpr Input
54        Structure+mass(db): tpr tpb tpa gro g96 pdb
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56       -n index.ndx Input, Opt.
57        Index file
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59       -o sori.xvg Output
60        xvgr/xmgr file
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62       -no snor.xvg Output
63        xvgr/xmgr file
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65       -ro sord.xvg Output
66        xvgr/xmgr file
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68       -co scum.xvg Output
69        xvgr/xmgr file
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71       -rc scount.xvg Output
72        xvgr/xmgr file
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OTHER OPTIONS

76       -[no]hno
77        Print help info and quit
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79       -[no]versionno
80        Print version info and quit
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82       -nice int 19
83        Set the nicelevel
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85       -b time 0
86        First frame (ps) to read from trajectory
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88       -e time 0
89        Last frame (ps) to read from trajectory
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91       -dt time 0
92        Only use frame when t MOD dt = first time (ps)
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94       -[no]wno
95        View output xvg, xpm, eps and pdb files
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97       -xvg enum xmgrace
98        xvg plot formatting:  xmgrace,  xmgr or  none
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100       -[no]comno
101        Use the center of mass as the reference postion
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103       -[no]v23no
104        Use the vector between atoms 2 and 3
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106       -rmin real 0
107        Minimum distance (nm)
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109       -rmax real 0.5
110        Maximum distance (nm)
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112       -cbin real 0.02
113        Binwidth for the cosine
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115       -rbin real 0.02
116        Binwidth for r (nm)
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118       -[no]pbcno
119        Check PBC for the center of mass calculation. Only necessary when your
120       reference group consists of several molecules.
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SEE ALSO

124       gromacs(7)
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126       More  information  about  GROMACS  is  available  at   <http://www.gro‐
127       macs.org/>.
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131                                Thu 26 Aug 2010                   g_sorient(1)
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