## Linux and UNIX Man Pages

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# g_dipoles(1) [debian man page]

```g_dipoles(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_dipoles(1)

NAME
g_dipoles - computes the total dipole plus fluctuations

VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS
g_dipoles  -en  ener.edr  -f  traj.xtc  -s topol.tpr -n index.ndx -o Mtot.xvg -eps epsilon.xvg -a aver.xvg -d dipdist.xvg -c dipcorr.xvg -g
gkr.xvg -adip adip.xvg -dip3d dip3d.xvg -cos cosaver.xvg -cmap cmap.xpm -q quadrupole.xvg -slab slab.xvg -[no]h -[no]version -nice  int	-b
time  -e  time  -dt  time  -[no]w -xvg enum -mu real -mumax real -epsilonRF real -skip int -temp real -corr enum -[no]pairs -ncos int -axis
string -sl int -gkratom int -gkratom2 int -rcmax real -[no]phi -nlevels int -ndegrees int -acflen int -[no]normalize -P	enum  -fitfn  enum
-ncskip int -beginfit real -endfit real

DESCRIPTION
g_dipoles  computes the total dipole plus fluctuations of a simulation system. From this you can compute e.g. the dielectric constant for
low-dielectric media.  For molecules with a net charge, the net charge is subtracted at center of mass of the molecule.

The file  Mtot.xvg contains the total dipole moment of a frame, the components as well as the norm of the vector.  The file  aver.xvg  con-
tains   |Mu|2   and | Mu |2 during the simulation.  The file  dipdist.xvg contains the distribution of dipole moments during the simulation
The value of  -mumax is used as the highest value in the distribution graph.

Furthermore, the dipole autocorrelation function will be computed when option  -corr is used. The output file name is given  with  the	-c
option.	 The  correlation functions can be averaged over all molecules ( mol), plotted per molecule separately ( molsep) or it can be com-
puted over the total dipole moment of the simulation box ( total).

Option  -g produces a plot of the distance dependent Kirkwood G-factor, as well as the average cosine of the angle between the dipoles as a
function  of  the  distance. The plot also includes gOO and hOO according to Nymand & Linse, J. Chem. Phys. 112 (2000) pp 6386-6395. In the
same plot, we also include the energy per scale computed by taking the inner product of the dipoles divided by the distance  to	the  third
power.

EXAMPLES

g_dipoles -corr mol -P1 -o dip_sqr -mu 2.273 -mumax 5.0 -nofft

This  will  calculate  the  autocorrelation  function  of the molecular dipoles using a first order Legendre polynomial of the angle of the
dipole vector and itself a time t later. For this calculation 1001 frames will be used. Further, the dielectric constant will be calculated
using  an  epsilonRF of infinity (default), temperature of 300 K (default) and an average dipole moment of the molecule of 2.273 (SPC). For
the distribution function a maximum of 5.0 will be used.

FILES
-en ener.edr Input, Opt.
Energy file

-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 Mtot.xvg Output
xvgr/xmgr file

-eps epsilon.xvg Output
xvgr/xmgr file

-a aver.xvg Output
xvgr/xmgr file

-d dipdist.xvg Output
xvgr/xmgr file

-c dipcorr.xvg Output, Opt.
xvgr/xmgr file

-g gkr.xvg Output, Opt.
xvgr/xmgr file

xvgr/xmgr file

-dip3d dip3d.xvg Output, Opt.
xvgr/xmgr file

-cos cosaver.xvg Output, Opt.
xvgr/xmgr file

-cmap cmap.xpm Output, Opt.
X PixMap compatible matrix file

xvgr/xmgr file

-slab slab.xvg Output, Opt.
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

-mu real -1
dipole of a single molecule (in Debye)

-mumax real 5
max dipole in Debye (for histrogram)

-epsilonRF real 0
epsilon of the reaction field used during the simulation,  needed  for	dielectric  constant  calculation.  WARNING:  0.0  means  infinity
(default)

-skip int 0
Skip steps in the output (but not in the computations)

-temp real 300
Average temperature of the simulation (needed for dielectric constant calculation)

-corr enum none
Correlation function to calculate:  none,  mol,  molsep or  total

-[no]pairsyes
Calculate |cos theta| between all pairs of molecules. May be slow

-ncos int 1
Must  be  1 or 2. Determines whether the cos is computed between all molecules in one group, or between molecules in two different groups.
This turns on the  -gkr flag.

-axis string Z
Take the normal on the computational box in direction X, Y or Z.

-sl int 10
Divide the box in nr slices.

-gkratom int 0
Use the n-th atom of a molecule (starting from 1) to calculate the distance between molecules rather than the center of charge (when 0) in
the calculation of distance dependent Kirkwood factors

-gkratom2 int 0
Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules

-rcmax real 0
Maximum  distance  to  use  in	the dipole orientation distribution (with ncos == 2). If zero, a criterion based on the box length will be
used.

-[no]phino
Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the  two	molecules  in  the
.xpm file from the  -cmap option. By default the cosine of the angle between the dipoles is plotted.

-nlevels int 20
Number of colors in the cmap output

-ndegrees int 90
Number of divisions on the  y-axis in the cmap output (for 180 degrees)

-acflen int -1
Length of the ACF, default is half the number of frames

-[no]normalizeyes
Normalize ACF

-P enum 0
Order of Legendre polynomial for ACF (0 indicates none):  0,  1,  2 or	3

-fitfn enum none
Fit function:  none,  exp,  aexp,  exp_exp,  vac,  exp5,  exp7,  exp9 or  erffit

-ncskip int 0
Skip N points in the output file of correlation functions

-beginfit real 0
Time where to begin the exponential fit of the correlation function

-endfit real -1
Time where to end the exponential fit of the correlation function, -1 is until the end