Provided by: gromacs-data_2018.1-1_all bug


       gmx-dipoles - Compute the total dipole plus fluctuations


          gmx dipoles [-en [<.edr>]] [-f [<.xtc/.trr/...>]] [-s [<.tpr>]]
                      [-n [<.ndx>]] [-o [<.xvg>]] [-eps [<.xvg>]] [-a [<.xvg>]]
                      [-d [<.xvg>]] [-c [<.xvg>]] [-g [<.xvg>]]
                      [-adip [<.xvg>]] [-dip3d [<.xvg>]] [-cos [<.xvg>]]
                      [-cmap [<.xpm>]] [-slab [<.xvg>]] [-b <time>] [-e <time>]
                      [-dt <time>] [-[no]w] [-xvg <enum>] [-mu <real>]
                      [-mumax <real>] [-epsilonRF <real>] [-skip <int>]
                      [-temp <real>] [-corr <enum>] [-[no]pairs] [-[no]quad]
                      [-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>] [-beginfit <real>] [-endfit <real>]


       gmx  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.


       gmx 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.


       Options to specify input files:

       -en [<.edr>] (ener.edr) (Optional)
              Energy file

       -f [<.xtc/.trr/…>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr>] (topol.tpr)
              Portable xdr run input file

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -o [<.xvg>] (Mtot.xvg)
              xvgr/xmgr file

       -eps [<.xvg>] (epsilon.xvg)
              xvgr/xmgr file

       -a [<.xvg>] (aver.xvg)
              xvgr/xmgr file

       -d [<.xvg>] (dipdist.xvg)
              xvgr/xmgr file

       -c [<.xvg>] (dipcorr.xvg) (Optional)
              xvgr/xmgr file

       -g [<.xvg>] (gkr.xvg) (Optional)
              xvgr/xmgr file

       -adip [<.xvg>] (adip.xvg) (Optional)
              xvgr/xmgr file

       -dip3d [<.xvg>] (dip3d.xvg) (Optional)
              xvgr/xmgr file

       -cos [<.xvg>] (cosaver.xvg) (Optional)
              xvgr/xmgr file

       -cmap [<.xpm>] (cmap.xpm) (Optional)
              X PixMap compatible matrix file

       -slab [<.xvg>] (slab.xvg) (Optional)
              xvgr/xmgr file

       Other options:

       -b <time> (0)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
              xvg plot formatting: xmgrace, xmgr, 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, total

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

       -[no]quad (no)
              Take quadrupole into account

       -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 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]phi (no)
              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]normalize (yes)
              Normalize ACF

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

       -fitfn <enum> (none)
              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9

       -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



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