gmx-h2order - Compute the orientation of water molecules

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                    GMX-H2ORDER(1)

gmxh2order  computes  the  orientation  of  water  molecules with respect to the normal of the box. The
       program determines the average cosine of the angle between the dipole moment of water and an axis of  the
       box.  The box is divided in slices and the average orientation per slice is printed.  Each water molecule
       is assigned to a slice, per time frame, based on the position of the oxygen. When -nm is used, the  angle
       between  the water dipole and the axis from the center of mass to the oxygen is calculated instead of the
       angle between the dipole and a box axis.

       • The program assigns whole water molecules to a slice, based on the first atom of  three  in  the  index
         file  group.  It assumes an order O,H,H. Name is not important, but the order is. If this demand is not
         met, assigning molecules to slices is different.

       gmx-h2order - Compute the orientation of water molecules

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-n[<.ndx>](index.ndx)
              Index file

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

       -s[<.tpr>](topol.tpr)
              Portable xdr run input file

       Options to specify output files:

       -o[<.xvg>](order.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

       -d<enum>(Z)
              Take the normal on the membrane in direction X, Y or Z.: Z, Y, X

       -sl<int>(0)
              Calculate order parameter as function of boxlength, dividing the box in this number of slices.

gmx(1)

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

          gmx h2order [-f[<.xtc/.trr/...>]] [-n[<.ndx>]] [-nm[<.ndx>]]
                      [-s[<.tpr>]] [-o[<.xvg>]] [-b<time>] [-e<time>]
                      [-dt<time>] [-[no]w] [-xvg<enum>] [-d<enum>]
                      [-sl<int>]