gmx-order - Compute the order parameter per atom for carbon tails

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                      GMX-ORDER(1)

gmxorder computes the order parameter per atom for carbon tails. For atom i the vector i-1, i+1 is used
       together with an axis.  The index file should contain only the groups to be used for  calculations,  with
       each  group of equivalent carbons along the relevant acyl chain in its own group. There should not be any
       generic groups (like System, Protein) in the index file to avoid  confusing  the  program  (this  is  not
       relevant to tetrahedral order parameters however, which only work for water anyway).

       gmxorder can also give all diagonal elements of the order tensor and even calculate the deuterium order
       parameter Scd (default). If the option -szonly is given, only one order tensor  component  (specified  by
       the  -d  option)  is  given  and  the  order parameter per slice is calculated as well. If -szonly is not
       selected, all diagonal elements and the deuterium order parameter is given.

       The tetrahedrality order parameters can be determined around  an  atom.  Both  angle  an  distance  order
       parameters  are  calculated. See P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.  for more
       details.

       • This tool only works for saturated carbons and united atom force fields.

       • For anything else, it is highly recommended to use a different analysis method!

       • The option -unsat claimed to do analysis for unsaturated carbons

       • this but hasn't worked ever since it was added and has thus been removed.

       gmx-order - Compute the order parameter per atom for carbon tails

       Options to specify input files:

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

       -nr[<.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

       -od[<.xvg>](deuter.xvg)
              xvgr/xmgr file

       -ob[<.pdb>](eiwit.pdb)(Optional)
              Protein data bank file

       -os[<.xvg>](sliced.xvg)
              xvgr/xmgr file

       -Sg[<.xvg>](sg-ang.xvg)(Optional)
              xvgr/xmgr file

       -Sk[<.xvg>](sk-dist.xvg)(Optional)
              xvgr/xmgr file

       -Sgsl[<.xvg>](sg-ang-slice.xvg)(Optional)
              xvgr/xmgr file

       -Sksl[<.xvg>](sk-dist-slice.xvg)(Optional)
              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)
              Direction of the normal on the membrane: z, x, y

       -sl<int>(1)
              Calculate order parameter as function of box length, dividing the box into this number of slices.

       -[no]szonly(no)
              Only give Sz element of order tensor. (axis can be specified with -d)

       -[no]permolecule(no)
              Compute per-molecule Scd order parameters

       -[no]radial(no)
              Compute a radial membrane normal

       -[no]calcdist(no)
              Compute distance from a reference

gmx(1)

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

          gmx order [-f[<.xtc/.trr/...>]] [-n[<.ndx>]] [-nr[<.ndx>]]
                    [-s[<.tpr>]] [-o[<.xvg>]] [-od[<.xvg>]] [-ob[<.pdb>]]
                    [-os[<.xvg>]] [-Sg[<.xvg>]] [-Sk[<.xvg>]]
                    [-Sgsl[<.xvg>]] [-Sksl[<.xvg>]] [-b<time>] [-e<time>]
                    [-dt<time>] [-[no]w] [-xvg<enum>] [-d<enum>] [-sl<int>]
                    [-[no]szonly] [-[no]permolecule] [-[no]radial]
                    [-[no]calcdist]