g_dipoles(1)

1g_dipoles(1)              GROMACS suite, VERSION 4.5              g_dipoles(1)
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NAME

6       g_dipoles - computes the total dipole plus fluctuations
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8       VERSION 4.5
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SYNOPSIS

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

22       g_dipoles  computes  the total dipole plus fluctuations of a simulation
23       system. From this you can compute e.g. the dielectric constant for  low
24       dielectric  media.   For molecules with a net charge, the net charge is
25       subtracted at center of mass of the molecule.
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28       The file Mtot.xvg contains the total dipole moment of a frame, the com‐
29       ponents  as well as the norm of the vector.  The file aver.xvg contains
30       |Mu|2  and | Mu |2 during the simulation.  The  file  dipdist.xvg  con‐
31       tains  the  distribution  of  dipole  moments during the simulation The
32       mu_max is used as the highest value in the distribution graph.
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35       Furthermore the dipole autocorrelation function will be  computed  when
36       option  -corr  is  used.  The  output  file  name is given with the  -c
37       option.  The correlation functions can be averaged over all molecules (
38       mol),  plotted  per molecule separately ( molsep) or it can be computed
39       over the total dipole moment of the simulation box ( total).
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42       Option  -g produces a plot of the distance dependent Kirkwood G-factor,
43       as  well  as  the  average cosine of the angle between the dipoles as a
44       function of the distance. The plot also includes gOO and hOO  according
45       to  Nymand  &  Linse,  JCP 112 (2000) pp 6386-6395. In the same plot we
46       also include the energy per scale computed by taking the inner  product
47       of the dipoles divided by the distance to the third power.
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53       EXAMPLES
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56       g_dipoles -corr mol -P1 -o dip_sqr -mu 2.273 -mumax 5.0 -nofft
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59       This  will  calculate  the  autocorrelation  function  of the molecular
60       dipoles using a first order Legendre polynomial of  the  angle  of  the
61       dipole  vector  and  itself  a  time t later. For this calculation 1001
62       frames will be used. Further the dielectric constant will be calculated
63       using  an  epsilonRF  of  infinity  (default),  temperature  of  300  K
64       (default) and an average dipole moment of the molecule of 2.273  (SPC).
65       For the distribution function a maximum of 5.0 will be used.
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FILES

68       -en ener.edr Input, Opt.
69        Energy file
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71       -f traj.xtc Input
72        Trajectory: xtc trr trj gro g96 pdb cpt
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74       -s topol.tpr Input
75        Run input file: tpr tpb tpa
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77       -n index.ndx Input, Opt.
78        Index file
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80       -o Mtot.xvg Output
81        xvgr/xmgr file
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83       -eps epsilon.xvg Output
84        xvgr/xmgr file
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86       -a aver.xvg Output
87        xvgr/xmgr file
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89       -d dipdist.xvg Output
90        xvgr/xmgr file
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92       -c dipcorr.xvg Output, Opt.
93        xvgr/xmgr file
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95       -g gkr.xvg Output, Opt.
96        xvgr/xmgr file
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98       -adip adip.xvg Output, Opt.
99        xvgr/xmgr file
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101       -dip3d dip3d.xvg Output, Opt.
102        xvgr/xmgr file
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104       -cos cosaver.xvg Output, Opt.
105        xvgr/xmgr file
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107       -cmap cmap.xpm Output, Opt.
108        X PixMap compatible matrix file
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110       -q quadrupole.xvg Output, Opt.
111        xvgr/xmgr file
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113       -slab slab.xvg Output, Opt.
114        xvgr/xmgr file
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OTHER OPTIONS

118       -[no]hno
119        Print help info and quit
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121       -[no]versionno
122        Print version info and quit
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124       -nice int 19
125        Set the nicelevel
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127       -b time 0
128        First frame (ps) to read from trajectory
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130       -e time 0
131        Last frame (ps) to read from trajectory
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133       -dt time 0
134        Only use frame when t MOD dt = first time (ps)
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136       -[no]wno
137        View output xvg, xpm, eps and pdb files
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139       -xvg enum xmgrace
140        xvg plot formatting:  xmgrace,  xmgr or  none
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142       -mu real -1
143        dipole of a single molecule (in Debye)
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145       -mumax real 5
146        max dipole in Debye (for histrogram)
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148       -epsilonRF real 0
149        epsilon  of  the reaction field used during the simulation, needed for
150       dielectric constant calculation. WARNING: 0.0 means infinity (default)
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152       -skip int 0
153        Skip steps in the output (but not in the computations)
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155       -temp real 300
156        Average temperature of the simulation (needed for dielectric  constant
157       calculation)
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159       -corr enum none
160        Correlation function to calculate:  none,  mol,  molsep or  total
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162       -[no]pairsyes
163        Calculate |cos theta| between all pairs of molecules. May be slow
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165       -ncos int 1
166        Must  be  1  or  2. Determines whether the cos is computed between all
167       mole cules in one group, or between molecules in two different  groups.
168       This turns on the -gkr flag.
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170       -axis string Z
171        Take the normal on the computational box in direction X, Y or Z.
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173       -sl int 10
174        Divide the box in nr slices.
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176       -gkratom int 0
177        Use  the  n-th  atom  of a molecule (starting from 1) to calculate the
178       distance between molecules rather than the center of charge (when 0) in
179       the calculation of distance dependent Kirkwood factors
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181       -gkratom2 int 0
182        Same  as  previous  option  in  case ncos = 2, i.e. dipole interaction
183       between two groups of molecules
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185       -rcmax real 0
186        Maximum distance to use in the dipole orientation  distribution  (with
187       ncos == 2). If zero, a criterium based on the box length will be used.
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189       -[no]phino
190        Plot  the  'torsion  angle'  defined as the rotation of the two dipole
191       vectors around the distance vector between the two molecules in the xpm
192       file  from the -cmap option. By default the cosine of the angle between
193       the dipoles is plotted.
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195       -nlevels int 20
196        Number of colors in the cmap output
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198       -ndegrees int 90
199        Number of divisions on the y-axis in the camp output (for 180 degrees)
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201       -acflen int -1
202        Length of the ACF, default is half the number of frames
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204       -[no]normalizeyes
205        Normalize ACF
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207       -P enum 0
208        Order of Legendre polynomial for ACF (0 indicates none):  0,  1,  2 or
209       3
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211       -fitfn enum none
212        Fit  function:   none,   exp,   aexp,   exp_exp,  vac,  exp5,  exp7 or
213       exp9
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215       -ncskip int 0
216        Skip N points in the output file of correlation functions
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218       -beginfit real 0
219        Time where to begin the exponential fit of the correlation function
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221       -endfit real -1
222        Time where to end the exponential fit of the correlation function,  -1
223       is until the end
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO