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)