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g_order(1) [debian man page]

g_order(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					g_order(1)

NAME

       g_order - computes the order parameter per atom for carbon tails

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_order	-f  traj.xtc  -n  index.ndx -nr index.ndx -s topol.tpr -o order.xvg -od deuter.xvg -ob eiwit.pdb -os sliced.xvg -Sg sg-ang.xvg -Sk
       sk-dist.xvg -Sgsl sg-ang-slice.xvg -Sksl sk-dist-slice.xvg -[no]h -[no]version -nice int -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

       Compute 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).

       The program 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 cal-
       culated 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.

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input
	Index file

       -nr index.ndx Input
	Index file

       -s topol.tpr Input
	Run input file: tpr tpb tpa

       -o order.xvg Output
	xvgr/xmgr file

       -od deuter.xvg Output
	xvgr/xmgr file

       -ob eiwit.pdb Output
	Protein data bank file

       -os sliced.xvg Output
	xvgr/xmgr file

       -Sg sg-ang.xvg Output, Opt.
	xvgr/xmgr file

       -Sk sk-dist.xvg Output, Opt.
	xvgr/xmgr file

       -Sgsl sg-ang-slice.xvg Output, Opt.
	xvgr/xmgr file

       -Sksl sk-dist-slice.xvg Output, Opt.
	xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 19
	Set the nicelevel

       -b time 0
	First frame (ps) to read from trajectory

       -e time 0
	Last frame (ps) to read from trajectory

       -dt time 0
	Only use frame when t MOD dt = first time (ps)

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -d enum z
	Direction of the normal on the membrane:  z,  x or  y

       -sl int 1
	Calculate order parameter as function of box length, dividing the box in nr slices.

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

       -[no]unsatno
	Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters.

       -[no]permoleculeno
	Compute per-molecule Scd order parameters

       -[no]radialno
	Compute a radial membrane normal

       -[no]calcdistno
	Compute distance from a reference (currently defined only for radial and permolecule)

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011							g_order(1)

Check Out this Related Man Page

g_sorient(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_sorient(1)

NAME

       g_sorient - analyzes solvent orientation around solutes

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_sorient -f traj.xtc -s topol.tpr -n index.ndx -o sori.xvg -no snor.xvg -ro sord.xvg -co scum.xvg -rc scount.xvg -[no]h -[no]version -nice
       int -b time -e time -dt time -[no]w -xvg enum -[no]com -[no]v23 -rmin real -rmax real -cbin real -rbin real -[no]pbc

DESCRIPTION

	g_sorient 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:

       theta1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3.

       theta2:	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  sol-
       vent molecule.  Only solvent molecules between  -rmin and  -rmax are considered for  -o and  -no each frame.

	-o: distribtion of cos(theta1) for rmin=r=rmax.

	-no: distribution of cos(theta2) for rmin=r=rmax.

	-ro: cos(theta1) and 3cos2(theta2)-1 as a function of the distance.

	-co: the sum over all solvent molecules within distance r of cos(theta1) and 3cos2(theta2)-1 as a function of r.

	-rc: the distribution of the solvent molecules as a function of r

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
	Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
	Index file

       -o sori.xvg Output
	xvgr/xmgr file

       -no snor.xvg Output
	xvgr/xmgr file

       -ro sord.xvg Output
	xvgr/xmgr file

       -co scum.xvg Output
	xvgr/xmgr file

       -rc scount.xvg Output
	xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 19
	Set the nicelevel

       -b time 0
	First frame (ps) to read from trajectory

       -e time 0
	Last frame (ps) to read from trajectory

       -dt time 0
	Only use frame when t MOD dt = first time (ps)

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -[no]comno
	Use the center of mass as the reference postion

       -[no]v23no
	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]pbcno
	Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						      g_sorient(1)
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