g_h2order (1) - Linux Manuals

g_h2order: computes the orientation of water molecules


g_h2order - computes the orientation of water molecules



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


Compute the orientation of water molecules with respect to the normal of the box. The program determines the average cosine of the angle between de 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.


-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 


 Print help 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)

 View output xvg, xpm, eps and pdb files

 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-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.


- The program assigns whole water molecules to a slice, based on the firstatom 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.



More information about GROMACS is available at <http://www.gromacs.org/>.