gmx-h2order - Online in the Cloud

PROGRAM:

NAME

gmx-h2order - Compute the orientation of water molecules

SYNOPSIS

gmx h2order [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-nm [<.ndx>]]
[-s [<.tpr>]] [-o [<.xvg>]] [-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 files:

-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng

-n [<.ndx>] (index.ndx)
Index file

-nm [<.ndx>] (index.ndx) (Optional)
Index file

-s [<.tpr>] (topol.tpr)
Portable xdr run input file

Options to specify output files:

-o [<.xvg>] (order.xvg)
xvgr/xmgr file

Other options:

-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>
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.

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