Provided by: gromacs-data_2019.3-2_all bug

NAME

       gmx-sorient - Analyze solvent orientation around solutes

SYNOPSIS

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

DESCRIPTION

       gmx sorient analyzes solvent orientation around solutes.  It calculates two angles between
       the vector from one or more  reference  positions  to  the  first  atom  of  each  solvent
       molecule:

          · theta_1: the angle with the vector from the first atom of the solvent molecule to the
            midpoint between atoms 2 and 3.

          · theta_2: the angle with the normal of the solvent plane, defined by  the  same  three
            atoms, or, when the option -v23 is set, the angle with the vector between atoms 2 and
            3.

       The reference can be a set of atoms or the center of mass of a set of atoms. The group  of
       solvent  atoms  should  consist  of  3 atoms per solvent molecule.  Only solvent molecules
       between -rmin and -rmax are considered for -o and -no each frame.

       -o: distribution of cos(theta_1) for rmin<=r<=rmax.

       -no: distribution of cos(theta_2) for rmin<=r<=rmax.

       -ro: <cos(theta_1)> and <3cos(^2theta_2)-1> as a function of the distance.

       -co:  the  sum  over  all  solvent  molecules  within  distance  r  of  cos(theta_1)   and
       3cos(^2(theta_2)-1) as a function of r.

       -rc: the distribution of the solvent molecules as a function of r

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/…>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/…>] (topol.tpr)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -o [<.xvg>] (sori.xvg)
              xvgr/xmgr file

       -no [<.xvg>] (snor.xvg)
              xvgr/xmgr file

       -ro [<.xvg>] (sord.xvg)
              xvgr/xmgr file

       -co [<.xvg>] (scum.xvg)
              xvgr/xmgr file

       -rc [<.xvg>] (scount.xvg)
              xvgr/xmgr file

       Other options:

       -b <time> (0)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -[no]com (no)
              Use the center of mass as the reference position

       -[no]v23 (no)
              Use the vector between atoms 2 and 3

       -rmin <real> (0)
              Minimum distance (nm)

       -rmax <real> (0.5)
              Maximum distance (nm)

       -cbin <real> (0.02)
              Binwidth for the cosine

       -rbin <real> (0.02)
              Binwidth for r (nm)

       -[no]pbc (no)
              Check  PBC  for  the center of mass calculation. Only necessary when your reference
              group consists of several molecules.

SEE ALSO

       gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

       2019, GROMACS development team