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       g_dipoles - computes the total dipole plus fluctuations

       VERSION 4.0.1


       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


       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

       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.


       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.


       -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


        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)

        View output xvg, xpm, eps and pdb files

        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

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

        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.

        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

        Normalize ACF

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

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

       -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



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                                Thu 16 Oct 2008                   g_dipoles(1)