NAME
g_sorient - analyzes solvent orientation around solutes
VERSION 4.0.1
SYNOPSIS
g_sorient -f traj.xtc -s topol.tpr -n index.ndx -o sori.xvg -no
snor.xvg -ro sord.xvg -co scum.xvg -rc scount.xvg -[no]h -nice int -b
time -e time -dt time -[no]w -[no]xvgr -[no]com -[no]v23 -rmin real
-rmax real -cbin real -rbin real -[no]pbc
DESCRIPTION
g_sorient analyzes solvent orientation around solutes. It calculates
two angles between the vector from one or more reference positions to
the first atom of each solvent molecule: theta1: the angle with the
vector from the first atom of the solvent molecule to the midpoint
between atoms 2 and 3.
theta2: the angle with the normal of the solvent plane, defined by the
same three atoms, or when the option -v23 is set the angle with the
vector between atoms 2 and 3.
The reference can be a set of atoms or the center of mass of a set of
atoms. The group of solvent atoms should consist of 3 atoms per solvent
molecule. Only solvent molecules between -rmin and -rmax are
considered for -o and -no each frame.
-o: distribtion of cos(theta1) for rmin=r=rmax.
-no: distribution of cos(theta2) for rmin=r=rmax.
-ro: cos(theta1) and 3cos2(theta2)-1 as a function of the distance.
-co: the sum over all solvent molecules within distance r of
cos(theta1) and 3cos2(theta2)-1 as a function of r.
-rc: the distribution of the solvent molecules as a function of r
FILES
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt.
Index file
-o sori.xvg Output
xvgr/xmgr file
-no snor.xvg Output
xvgr/xmgr file
-ro sord.xvg Output
xvgr/xmgr file
-co scum.xvg Output
xvgr/xmgr file
-rc scount.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
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)
-[no]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-[no]comno
Use the center of mass as the reference postion
-[no]v23no
Use the vector between atoms 2 and 3
-rmin real 0
Minimum distance (nm)
-rmax real 0.5
Maximum distance (nm)
-cbin real 0.02
Binwidth for the cosine
-rbin real 0.02
Binwidth for r (nm)
-[no]pbcno
Check PBC for the center of mass calculation. Only necessary when your
reference group consists of several molecules.
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_sorient(1)