g_h2order

Main Table of Contents

VERSION 4.6.5
Mon 2 Dec 2013


Description

g_h2order computes the orientation of water molecules with respect to the normal of the box. The program determines the average cosine of the angle between the dipole moment of water and an axis of the box. The box is divided in slices and the average orientation per slice is printed. Each water molecule is assigned to a slice, per time frame, based on the position of the oxygen. When -nm is used, the angle between the water dipole and the axis from the center of mass to the oxygen is calculated instead of the angle between the dipole and a box axis.

Files

optionfilenametypedescription
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-n index.ndx Input Index file
-nm index.ndx Input, Opt. Index file
-s topol.tpr Input Run input file: tpr tpb tpa
-o order.xvg Output xvgr/xmgr file

Other options

optiontypedefaultdescription
-[no]h bool no Print help info and quit
-[no]version bool no 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]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-d string Z Take the normal on the membrane in direction X, Y or Z.
-sl int 0 Calculate order parameter as function of boxlength, dividing the box in this number of slices.

Known problems


http://www.gromacs.org
gromacs@gromacs.org