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NAME

       g_dipoles - computes the total dipole plus fluctuations

       VERSION 4.0.1

SYNOPSIS

       g_dipoles  -enx  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 -nice int -b time -e  time  -dt
       time  -[no]w  -[no]xvgr  -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
       contains   |Mu|2   and   |Mu|  2  during  the  simulation.   The   file
       dipdist.xvg  contains  the  distribution  of  dipole moments during the
       simulation The mu_max 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 seperately ( molsep) or it can  be  computed
       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, JCP 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

       -enx ener.edr Input, Opt.
        Energy file: edr ene

       -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

       -adip adip.xvg Output, Opt.
        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

       -q quadrupole.xvg Output, Opt.
        xvgr/xmgr file

       -slab slab.xvg Output, Opt.
        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

       -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
       dieclectric 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
       mole  cules 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 criterium 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 camp 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  or
       exp9

       -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 till the end

SEE ALSO

       gromacs(7)

       More     information     about     GROMACS     is     available      at
       <http://www.gromacs.org/>.

                                Thu 16 Oct 2008                   g_dipoles(1)