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

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_spol\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-o" " scdist.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 "\-refat" " int "
.BI "\-rmin" " real "
.BI "\-rmax" " real "
.BI "\-dip" " real "
.BI "\-bw" " real "
.SH DESCRIPTION
\&\fB g_spol\fR analyzes dipoles around a solute; it is especially useful
\&for polarizable water. A group of reference atoms, or a center
\&of mass reference (option \fB \-com\fR) and a group of solvent
\&atoms is required. The program splits the group of solvent atoms
\&into molecules. For each solvent molecule the distance to the
\&closest atom in reference group or to the COM is determined.
\&A cumulative distribution of these distances is plotted.
\&For each distance between \fB \-rmin\fR and \fB \-rmax\fR
\&the inner product of the distance vector
\&and the dipole of the solvent molecule is determined.
\&For solvent molecules with net charge (ions), the net charge of the ion
\&is subtracted evenly from all atoms in the selection of each ion.
\&The average of these dipole components is printed.
\&The same is done for the polarization, where the average dipole is
\&subtracted from the instantaneous dipole. The magnitude of the average
\&dipole is set with the option \fB \-dip\fR, the direction is defined
\&by the vector from the first atom in the selected solvent group
\&to the midpoint between the second and the third atom.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

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

.BI "\-o" " scdist.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 "\-refat"  " int" " 1" 
 The reference atom of the solvent molecule

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

.BI "\-rmax"  " real" " 0.32  " 
 Maximum distance (nm)

.BI "\-dip"  " real" " 0     " 
 The average dipole (D)

.BI "\-bw"  " real" " 0.01  " 
 The bin width

.SH SEE ALSO
.BR gromacs(7)

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