table of contents
g_hydorder(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_hydorder(1) |
NAME¶
g_hydorder - computes tetrahedrality parameters around a given atom VERSION 4.5.4-dev-20110404-bc5695cSYNOPSIS¶
g_hydorder -f traj.xtc -n index.ndx -s topol.tpr -o intf.xpm -or raw.out -Spect intfspect.out -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -d enum -bw real -sgang1 real -sgang2 real -tblock int -nlevel intDESCRIPTION¶
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. This application calculates the orderparameter in a 3d-mesh in the box, and with 2 phases in the box gives the user the option to define a 2D interface in time separating the faces by specifying parameters -sgang1 and -sgang2 (It is important to select these judiciously)FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Index file
Run input file: tpr tpb tpa
X PixMap compatible matrix file
Generic output file
Generic output 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
Direction of the normal on the membrane: z, x or y
Binwidth of box mesh
tetrahedral angle parameter in Phase 1 (bulk)
tetrahedral angle parameter in Phase 2 (bulk)
Number of frames in one time-block average
Number of Height levels in 2D - XPixMaps
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |