g_sorient_d (1) - Linux Manuals

g_sorient_d: analyzes solvent orientation around solutes

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.