.TH g_sorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_sorient - analyzes solvent orientation around solutes

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_sorient\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-o" " sori.xvg "
.BI "\-no" " snor.xvg "
.BI "\-ro" " sord.xvg "
.BI "\-co" " scum.xvg "
.BI "\-rc" " scount.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-[no]com" ""
.BI "\-[no]v23" ""
.BI "\-rmin" " real "
.BI "\-rmax" " real "
.BI "\-cbin" " real "
.BI "\-rbin" " real "
.BI "\-[no]pbc" ""
.SH DESCRIPTION
\&\fB g_sorient\fR 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 \fB \-v23\fR 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 \fB \-rmin\fR and \fB \-rmax\fR are
\&considered for \fB \-o\fR and \fB \-no\fR each frame.


\&\fB \-o\fR: distribtion of cos(theta1) for rmin=r=rmax.


\&\fB \-no\fR: distribution of cos(theta2) for rmin=r=rmax.


\&\fB \-ro\fR: cos(theta1) and 3cos2(theta2)\-1 as a function of the
\&distance.


\&\fB \-co\fR: the sum over all solvent molecules within distance r
\&of cos(theta1) and 3cos2(theta2)\-1 as a function of r.


\&\fB \-rc\fR: the distribution of the solvent molecules as a function of r
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-o" " sori.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-no" " snor.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-ro" " sord.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-co" " scum.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-rc" " scount.xvg" 
.B Output
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]com"  "no    "
 Use the center of mass as the reference postion

.BI "\-[no]v23"  "no    "
 Use the vector between atoms 2 and 3

.BI "\-rmin"  " real" " 0     " 
 Minimum distance (nm)

.BI "\-rmax"  " real" " 0.5   " 
 Maximum distance (nm)

.BI "\-cbin"  " real" " 0.02  " 
 Binwidth for the cosine

.BI "\-rbin"  " real" " 0.02  " 
 Binwidth for r (nm)

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

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.