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g_sorient

NAME

g_sorient VERSION 3.3_beta_20050823

SYNOPSIS

g_sorient -f traj.xtc -s topol.tpr -n index.ndx -o sori.xvg -no snor.xvg -ro sord.xvg -co scum.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]com -rmin real -rmax real -bin 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.

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 3cos2(theta2)-1 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.

FILES

-f traj.xtc Input
 Generic trajectory: xtc trr trj gro g96 pdb 

-s topol.tpr Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb xml 

-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 

OTHER OPTIONS

-[no]h no
 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]w no
 View output xvg, xpm, eps and pdb files

-[no]xvgr yes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-[no]com no
 Use the center of mass as the reference postion

-rmin real 0
 Minimum distance

-rmax real 0.5
 Maximum distance

-bin real 0.02
 Binwidth

-[no]pbc no
 Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.