gmx-sorient - Analyze solvent orientation around solutes

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                    GMX-SORIENT(1)

gmxsorient  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

       gmx-sorient - Analyze solvent orientation around solutes

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-s[<.tpr/.gro/...>](topol.tpr)
              Structure+mass(db): tprgrog96pdb 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.

gmx(1)

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

          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]