g_spol(1)
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
- More information about GROMACS is available at <http://www.gromacs.org/>.