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g_order

NAME

g_order - computes the order parameter per atom for carbon tails

VERSION 4.5

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 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 

-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 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.

-[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/>.