g_sorient(1) - Linux man page
Name
g_sorient - analyzes solvent orientation around solutesVERSION 4.5.4-dev-20110404-bc5695c
Synopsis
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/>.