1GMX-DIPOLES(1) GROMACS GMX-DIPOLES(1)
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6 gmx-dipoles - Compute the total dipole plus fluctuations
7
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
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.
28 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.
34 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).
40 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.
47 EXAMPLES
49 gmx dipoles -corr mol -P 1 -o dip_sqr -mu 2.273 -mumax 5.0
51 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.
59
61 Options to specify input files:
62 -en [<.edr>] (ener.edr) (Optional)
64 Energy file
65 -f [<.xtc/.trr/...>] (traj.xtc)
67 Trajectory: xtc trr cpt gro g96 pdb tng
68 -s [<.tpr>] (topol.tpr)
70 Portable xdr run input file
71 -n [<.ndx>] (index.ndx) (Optional)
73 Index file
74 Options to specify output files:
76 -o [<.xvg>] (Mtot.xvg)
78 xvgr/xmgr file
79 -eps [<.xvg>] (epsilon.xvg)
81 xvgr/xmgr file
82 -a [<.xvg>] (aver.xvg)
84 xvgr/xmgr file
85 -d [<.xvg>] (dipdist.xvg)
87 xvgr/xmgr file
88 -c [<.xvg>] (dipcorr.xvg) (Optional)
90 xvgr/xmgr file
91 -g [<.xvg>] (gkr.xvg) (Optional)
93 xvgr/xmgr file
94 -adip [<.xvg>] (adip.xvg) (Optional)
96 xvgr/xmgr file
97 -dip3d [<.xvg>] (dip3d.xvg) (Optional)
99 xvgr/xmgr file
100 -cos [<.xvg>] (cosaver.xvg) (Optional)
102 xvgr/xmgr file
103 -cmap [<.xpm>] (cmap.xpm) (Optional)
105 X PixMap compatible matrix file
106 -slab [<.xvg>] (slab.xvg) (Optional)
108 xvgr/xmgr file
109 Other options:
111 -b <time> (0)
113 Time of first frame to read from trajectory (default unit ps)
114 -e <time> (0)
116 Time of last frame to read from trajectory (default unit ps)
117 -dt <time> (0)
119 Only use frame when t MOD dt = first time (default unit ps)
120 -[no]w (no)
122 View output .xvg, .xpm, .eps and .pdb files
123 -xvg <enum> (xmgrace)
125 xvg plot formatting: xmgrace, xmgr, none
126 -mu <real> (-1)
128 dipole of a single molecule (in Debye)
129 -mumax <real> (5)
131 max dipole in Debye (for histogram)
132 -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 -skip <int> (0)
139 Skip steps in the output (but not in the computations)
140 -temp <real> (300)
142 Average temperature of the simulation (needed for dielectric
143 constant calculation)
144 -corr <enum> (none)
146 Correlation function to calculate: none, mol, molsep, total
147 -[no]pairs (yes)
149 Calculate |cos(theta)| between all pairs of molecules. May be
150 slow
151 -[no]quad (no)
153 Take quadrupole into account
154 -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 -axis <string> (Z)
161 Take the normal on the computational box in direction X, Y or Z.
162 -sl <int> (10)
164 Divide the box into this number of slices.
165 -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 -gkratom2 <int> (0)
173 Same as previous option in case ncos = 2, i.e. dipole interac‐
174 tion between two groups of molecules
175 -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 -[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 co‐
185 sine of the angle between the dipoles is plotted.
186 -nlevels <int> (20)
188 Number of colors in the cmap output
189 -ndegrees <int> (90)
191 Number of divisions on the y-axis in the cmap output (for 180
192 degrees)
193 -acflen <int> (-1)
195 Length of the ACF, default is half the number of frames
196 -[no]normalize (yes)
198 Normalize ACF
199 -P <enum> (0)
201 Order of Legendre polynomial for ACF (0 indicates none): 0, 1,
202 2, 3
203 -fitfn <enum> (none)
205 Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
206 -beginfit <real> (0)
208 Time where to begin the exponential fit of the correlation func‐
209 tion
210 -endfit <real> (-1)
212 Time where to end the exponential fit of the correlation func‐
213 tion, -1 is until the end
214
216 gmx(1)
217 More information about GROMACS is available at <‐
219 http://www.gromacs.org/>.
220
222 2022, GROMACS development team
2232022.3 Sep 02, 2022 GMX-DIPOLES(1)