NAME
g_order - computes the order parameter per atom for carbon tails
VERSION 4.0.1
SYNOPSIS
g_order -f traj.xtc -n index.ndx -s topol.tpr -o order.xvg -od
deuter.xvg -os sliced.xvg -Sg sg-ang.xvg -Sk sk-dist.xvg -[no]h -nice
int -b time -e time -dt time -[no]w -[no]xvgr -d enum -sl int
-[no]szonly -[no]unsat
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 has to
contain a group with all equivalent atoms in all tails for each atom
the order parameter has to be calculated for. 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 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.
FILES
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-n 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
-os sliced.xvg Output
xvgr/xmgr file
-Sg sg-ang.xvg Output
xvgr/xmgr file
-Sk sk-dist.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help 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
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-d enum z
Direction of the normal on the membrane: z, x or y
-sl int 1
Calculate order parameter as function of boxlength, 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.
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_order(1)