NAME

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

SYNOPSIS

          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]

DESCRIPTION

       gmx  order  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).

       gmx order 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.

OPTIONS

       Options to specify input files:

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

       -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

KNOWN ISSUES

       • 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.

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2023, GROMACS development team