g_sorient - analyzes solvent orientation around solutes
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
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
-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.
-o sori.xvg Output
-no snor.xvg Output
-ro sord.xvg Output
-co scum.xvg Output
-rc scount.xvg Output
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
Use the center of mass as the reference postion
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)
Check PBC for the center of mass calculation. Only necessary when your
reference group consists of several molecules.
More information about GROMACS is available at
Thu 16 Oct 2008 g_sorient(1)