gmx-spol(1) GROMACS Manual gmx-spol(1)NAMEgmx-spol - Analyze solvent dipole orientation and polarization around
solutes
SYNOPSIS
gmx spol [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
[-o [<.xvg>]] [-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
gmx spol analyzes dipoles around a solute; it is especially useful for
polarizable water. A group of reference atoms, or a center of mass ref‐
erence (option -com) and a group of solvent atoms is required. The pro‐
gram 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 deter‐
mined. 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.
OPTIONS
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-o [<.xvg>] (scdist.xvg) (Output)
xvgr/xmgr file
Other options:
-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]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[no]com (no)
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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-spol(1)
