g_sorient(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_sorient(1)
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 -[no]version -nice
int -b time -e time -dt time -[no]w -xvg enum -[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 sol-
vent 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
Print version 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
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
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 <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_sorient(1)