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GMX-ORDER(1)			    GROMACS			  GMX-ORDER(1)

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]unsat] [-[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, Pro-
       tein) 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 op-
       tion -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 deu-
       terium 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/^a|>] (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]unsat (no)
	      Calculate	 order	parameters  for	unsaturated carbons. Note that
	      this cannot be mixed with	normal order parameters.

       -[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

SEE ALSO
       gmx(1)

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

COPYRIGHT
       2020, GROMACS development team

2020.3				 Jul 09, 2020			  GMX-ORDER(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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