1GMX-SORIENT(1)                      GROMACS                     GMX-SORIENT(1)
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NAME

6       gmx-sorient - Analyze solvent orientation around solutes
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SYNOPSIS

9          gmx sorient [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                      [-o [<.xvg>]] [-no [<.xvg>]] [-ro [<.xvg>]]
11                      [-co [<.xvg>]] [-rc [<.xvg>]] [-b <time>] [-e <time>]
12                      [-dt <time>] [-[no]w] [-xvg <enum>] [-[no]com] [-[no]v23]
13                      [-rmin <real>] [-rmax <real>] [-cbin <real>]
14                      [-rbin <real>] [-[no]pbc]
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DESCRIPTION

17       gmx 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          · theta_1: the angle with the vector from the first atom of the sol‐
22            vent molecule to the midpoint between atoms 2 and 3.
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24          · theta_2: the angle with the normal of the solvent  plane,  defined
25            by  the  same  three  atoms,  or, when the option -v23 is set, the
26            angle with the 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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33       -o: distribution of cos(theta_1) for rmin<=r<=rmax.
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35       -no: distribution of cos(theta_2) for rmin<=r<=rmax.
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37       -ro:  <cos(theta_1)>  and <3cos(^2theta_2)-1> as a function of the dis‐
38       tance.
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40       -co:  the  sum  over  all  solvent  molecules  within  distance  r   of
41       cos(theta_1) and 3cos(^2(theta_2)-1) as a function of r.
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43       -rc: the distribution of the solvent molecules as a function of r
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OPTIONS

46       Options to specify input files:
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48       -f [<.xtc/.trr/…>] (traj.xtc)
49              Trajectory: xtc trr cpt gro g96 pdb tng
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51       -s [<.tpr/.gro/…>] (topol.tpr)
52              Structure+mass(db): tpr gro g96 pdb brk ent
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54       -n [<.ndx>] (index.ndx) (Optional)
55              Index file
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57       Options to specify output files:
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59       -o [<.xvg>] (sori.xvg)
60              xvgr/xmgr file
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62       -no [<.xvg>] (snor.xvg)
63              xvgr/xmgr file
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65       -ro [<.xvg>] (sord.xvg)
66              xvgr/xmgr file
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68       -co [<.xvg>] (scum.xvg)
69              xvgr/xmgr file
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71       -rc [<.xvg>] (scount.xvg)
72              xvgr/xmgr file
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74       Other options:
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76       -b <time> (0)
77              Time of first frame to read from trajectory (default unit ps)
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79       -e <time> (0)
80              Time of last frame to read from trajectory (default unit ps)
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82       -dt <time> (0)
83              Only use frame when t MOD dt = first time (default unit ps)
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85       -[no]w (no)
86              View output .xvg, .xpm, .eps and .pdb files
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88       -xvg <enum> (xmgrace)
89              xvg plot formatting: xmgrace, xmgr, none
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91       -[no]com (no)
92              Use the center of mass as the reference position
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94       -[no]v23 (no)
95              Use the vector between atoms 2 and 3
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97       -rmin <real> (0)
98              Minimum distance (nm)
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100       -rmax <real> (0.5)
101              Maximum distance (nm)
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103       -cbin <real> (0.02)
104              Binwidth for the cosine
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106       -rbin <real> (0.02)
107              Binwidth for r (nm)
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109       -[no]pbc (no)
110              Check  PBC  for  the  center of mass calculation. Only necessary
111              when your reference group consists of several molecules.
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SEE ALSO

114       gmx(1)
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116       More    information    about    GROMACS    is    available    at     <‐
117       http://www.gromacs.org/>.
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120       2019, GROMACS development team
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1252018.7                           May 29, 2019                   GMX-SORIENT(1)
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