gmx-h2order(1) GROMACS Manual gmx-h2order(1)NAMEgmx-h2order - Compute the orientation of water molecules
SYNOPSIS
gmx h2order [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-nm [<.ndx>]]
[-s [<.tpr/.tpb/...>]] [-o [<.xvg>]] [-nice <int>]
[-b <time>] [-e <time>] [-dt <time>] [-[no]w]
[-xvg <enum>] [-d <string>] [-sl <int>]
DESCRIPTION
gmx 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.
OPTIONS
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-n [<.ndx>] (index.ndx) (Input)
Index file
-nm [<.ndx>] (index.ndx) (Input, Optional)
Index file
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-o [<.xvg>] (order.xvg) (Output)
xvgr/xmgr file
Other options:
-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 (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, 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 ISSUES
- 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.
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-h2order(1)
