table of contents
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 tailsSYNOPSIS¶
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]calcdistDESCRIPTION¶
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).FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Index file
Index file
Run input file: tpr tpb tpa
xvgr/xmgr file
xvgr/xmgr file
Protein data bank file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Direction of the normal on the membrane: z, x or y
Calculate order parameter as function of box length, dividing the box in nr slices.
Only give Sz element of order tensor. (axis can be specified with -d)
Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters.
Compute per-molecule Scd order parameters
Compute a radial membrane normal
Compute distance from a reference (currently defined only for radial and permolecule)
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |