NAME¶

g_sorient - analyzes solvent orientation around solutes VERSION 4.5.4-dev-20110404-bc5695c

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 -[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

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 -[no]versionno
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) -[no]wno
View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none -[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/>.