g_sorient (1) - Linux Manuals

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/>.