Provided by: gromacs-data_4.6.5-1build1_all bug


       g_dipoles - computes the total dipole plus fluctuations

       VERSION 4.6.5


       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


         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 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
       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, 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.


        g_dipoles -corr mol -P 1 -o dip_sqr -mu 2.273 -mumax 5.0

       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.


       -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

       -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

        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)

        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 histogram)

       -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

        Calculate |cos(theta)| between all pairs of molecules. May be slow

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

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

       -sl int 10
        Divide the box into this number of 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

       -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.

        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

        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 this many 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



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                                          Mon 2 Dec 2013                             g_dipoles(1)