NAME
g_spol - analyzes solvent dipole orientation and polarization around
solutes
VERSION 4.0.1
SYNOPSIS
g_spol -f traj.xtc -s topol.tpr -n index.ndx -o scdist.xvg -[no]h -nice
int -b time -e time -dt time -[no]w -[no]xvgr -[no]com -refat int -rmin
real -rmax real -dip real -bw real
DESCRIPTION
g_spol analyzes dipoles around a solute; it is especially useful for
polarizable water. A group of reference atoms, or a center of mass
reference (option -com) 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 -rmin and -rmax the inner
product of the distance vector and the dipole of the solvent molecule
is determined. 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 -dip, 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.
FILES
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Run input file: tpr tpb tpa
-n index.ndx Input, Opt.
Index file
-o scdist.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
-refat int 1
The reference atom of the solvent molecule
-rmin real 0
Maximum distance (nm)
-rmax real 0.32
Maximum distance (nm)
-dip real 0
The average dipole (D)
-bw real 0.01
The bin width
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_spol(1)