1GMX-DIPOLES(1)                      GROMACS                     GMX-DIPOLES(1)
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NAME

6       gmx-dipoles - Compute the total dipole plus fluctuations
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SYNOPSIS

9          gmx dipoles [-en [<.edr>]] [-f [<.xtc/.trr/...>]] [-s [<.tpr>]]
10                      [-n [<.ndx>]] [-o [<.xvg>]] [-eps [<.xvg>]] [-a [<.xvg>]]
11                      [-d [<.xvg>]] [-c [<.xvg>]] [-g [<.xvg>]]
12                      [-adip [<.xvg>]] [-dip3d [<.xvg>]] [-cos [<.xvg>]]
13                      [-cmap [<.xpm>]] [-slab [<.xvg>]] [-b <time>] [-e <time>]
14                      [-dt <time>] [-[no]w] [-xvg <enum>] [-mu <real>]
15                      [-mumax <real>] [-epsilonRF <real>] [-skip <int>]
16                      [-temp <real>] [-corr <enum>] [-[no]pairs] [-[no]quad]
17                      [-ncos <int>] [-axis <string>] [-sl <int>]
18                      [-gkratom <int>] [-gkratom2 <int>] [-rcmax <real>]
19                      [-[no]phi] [-nlevels <int>] [-ndegrees <int>]
20                      [-acflen <int>] [-[no]normalize] [-P <enum>]
21                      [-fitfn <enum>] [-beginfit <real>] [-endfit <real>]
22

DESCRIPTION

24       gmx dipoles computes the total dipole plus fluctuations of a simulation
25       system. From this you can compute  e.g.  the  dielectric  constant  for
26       low-dielectric  media.  For molecules with a net charge, the net charge
27       is subtracted at center of mass of the molecule.
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29       The file Mtot.xvg contains the total dipole moment of a frame, the com‐
30       ponents  as well as the norm of the vector.  The file aver.xvg contains
31       <|mu|^2> and |<mu>|^2 during the simulation.  The file dipdist.xvg con‐
32       tains  the  distribution  of  dipole  moments during the simulation The
33       value of -mumax 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 option.
37       The correlation functions can be averaged  over  all  molecules  (mol),
38       plotted per molecule separately (molsep) or it can be computed over the
39       total dipole moment of the simulation box (total).
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41       Option -g produces a plot of the distance dependent Kirkwood  G-factor,
42       as  well  as  the  average cosine of the angle between the dipoles as a
43       function of the distance. The plot also includes gOO and hOO  according
44       to  Nymand & Linse, J. Chem. Phys. 112 (2000) pp 6386-6395. In the same
45       plot, we also include the energy per scale computed by taking the inner
46       product of the dipoles divided by the distance to the third power.
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48       EXAMPLES
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50       gmx dipoles -corr mol -P 1 -o dip_sqr -mu 2.273 -mumax 5.0
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52       This  will  calculate  the  autocorrelation  function  of the molecular
53       dipoles using a first order Legendre polynomial of  the  angle  of  the
54       dipole  vector  and  itself  a  time t later. For this calculation 1001
55       frames will be used. Further, the dielectric constant  will  be  calcu‐
56       lated  using  an -epsilonRF of infinity (default), temperature of 300 K
57       (default) and an average dipole moment of the molecule of 2.273  (SPC).
58       For the distribution function a maximum of 5.0 will be used.
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OPTIONS

61       Options to specify input files:
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63       -en [<.edr>] (ener.edr) (Optional)
64              Energy file
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66       -f [<.xtc/.trr/…>] (traj.xtc)
67              Trajectory: xtc trr cpt gro g96 pdb tng
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69       -s [<.tpr>] (topol.tpr)
70              Portable xdr run input file
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72       -n [<.ndx>] (index.ndx) (Optional)
73              Index file
74
75       Options to specify output files:
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77       -o [<.xvg>] (Mtot.xvg)
78              xvgr/xmgr file
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80       -eps [<.xvg>] (epsilon.xvg)
81              xvgr/xmgr file
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83       -a [<.xvg>] (aver.xvg)
84              xvgr/xmgr file
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86       -d [<.xvg>] (dipdist.xvg)
87              xvgr/xmgr file
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89       -c [<.xvg>] (dipcorr.xvg) (Optional)
90              xvgr/xmgr file
91
92       -g [<.xvg>] (gkr.xvg) (Optional)
93              xvgr/xmgr file
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95       -adip [<.xvg>] (adip.xvg) (Optional)
96              xvgr/xmgr file
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98       -dip3d [<.xvg>] (dip3d.xvg) (Optional)
99              xvgr/xmgr file
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101       -cos [<.xvg>] (cosaver.xvg) (Optional)
102              xvgr/xmgr file
103
104       -cmap [<.xpm>] (cmap.xpm) (Optional)
105              X PixMap compatible matrix file
106
107       -slab [<.xvg>] (slab.xvg) (Optional)
108              xvgr/xmgr file
109
110       Other options:
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112       -b <time> (0)
113              Time of first frame to read from trajectory (default unit ps)
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115       -e <time> (0)
116              Time of last frame to read from trajectory (default unit ps)
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118       -dt <time> (0)
119              Only use frame when t MOD dt = first time (default unit ps)
120
121       -[no]w (no)
122              View output .xvg, .xpm, .eps and .pdb files
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124       -xvg <enum> (xmgrace)
125              xvg plot formatting: xmgrace, xmgr, none
126
127       -mu <real> (-1)
128              dipole of a single molecule (in Debye)
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130       -mumax <real> (5)
131              max dipole in Debye (for histogram)
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133       -epsilonRF <real> (0)
134              epsilon of the reaction field used during the simulation, needed
135              for dielectric constant calculation. WARNING: 0.0 means infinity
136              (default)
137
138       -skip <int> (0)
139              Skip steps in the output (but not in the computations)
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141       -temp <real> (300)
142              Average  temperature  of  the  simulation (needed for dielectric
143              constant calculation)
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145       -corr <enum> (none)
146              Correlation function to calculate: none, mol, molsep, total
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148       -[no]pairs (yes)
149              Calculate |cos(theta)| between all pairs of  molecules.  May  be
150              slow
151
152       -[no]quad (no)
153              Take quadrupole into account
154
155       -ncos <int> (1)
156              Must  be 1 or 2. Determines whether the <cos(theta)> is computed
157              between all molecules in one group, or between molecules in  two
158              different groups. This turns on the -g flag.
159
160       -axis <string> (Z)
161              Take the normal on the computational box in direction X, Y or Z.
162
163       -sl <int> (10)
164              Divide the box into this number of slices.
165
166       -gkratom <int> (0)
167              Use  the  n-th atom of a molecule (starting from 1) to calculate
168              the distance between molecules rather than the center of  charge
169              (when  0) in the calculation of distance dependent Kirkwood fac‐
170              tors
171
172       -gkratom2 <int> (0)
173              Same as previous option in case ncos = 2, i.e.  dipole  interac‐
174              tion between two groups of molecules
175
176       -rcmax <real> (0)
177              Maximum  distance  to use in the dipole orientation distribution
178              (with ncos == 2). If zero, a criterion based on the  box  length
179              will be used.
180
181       -[no]phi (no)
182              Plot  the  ‘torsion  angle’  defined  as the rotation of the two
183              dipole vectors around the distance vector between the two  mole‐
184              cules  in  the  .xpm  file from the -cmap option. By default the
185              cosine of the angle between the dipoles is plotted.
186
187       -nlevels <int> (20)
188              Number of colors in the cmap output
189
190       -ndegrees <int> (90)
191              Number of divisions on the y-axis in the cmap  output  (for  180
192              degrees)
193
194       -acflen <int> (-1)
195              Length of the ACF, default is half the number of frames
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197       -[no]normalize (yes)
198              Normalize ACF
199
200       -P <enum> (0)
201              Order  of  Legendre polynomial for ACF (0 indicates none): 0, 1,
202              2, 3
203
204       -fitfn <enum> (none)
205              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
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207       -beginfit <real> (0)
208              Time where to begin the exponential fit of the correlation func‐
209              tion
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211       -endfit <real> (-1)
212              Time  where  to end the exponential fit of the correlation func‐
213              tion, -1 is until the end
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SEE ALSO

216       gmx(1)
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218       More    information    about    GROMACS    is    available    at     <‐
219       http://www.gromacs.org/>.
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222       2020, GROMACS development team
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2272019.6                           Feb 28, 2020                   GMX-DIPOLES(1)
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