10-24-2006
It's an average, not an instantaneous number.
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LEARN ABOUT DEBIAN
g_spol
g_spol(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_spol(1)
NAME
g_spol - analyzes solvent dipole orientation and polarization around solutes
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_spol -f traj.xtc -s topol.tpr -n index.ndx -o scdist.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[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 dis-
tances is plotted. For each distance between -rmin and -rmax the inner product of the distance vector and the dipole of the solvent mol-
ecule 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 -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
-[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
-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/>.
Mon 4 Apr 2011 g_spol(1)