g_h2order(1) - Linux man page

Name

g_h2order - computes the orientation of water molecules

VERSION 4.5.4-dev-20110404-bc5695c

Synopsis

g_h2order -f traj.xtc -n index.ndx -nm index.ndx -s topol.tpr -o order.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -dstring -sl int

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

-ftraj.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

-[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 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 nr slices.

Known Problems

- The program assigns whole water molecules to a slice, based on the first atom of three in the index file group. It assumes an order O,H,H. Name is not important, but the order is. If this demand is not met, assigning molecules to slices is different.