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
For molecules with a net charge, the net charge is subtracted at
center of mass of the molecule.
Mtot.xvg contains the total dipole moment of a frame, the
components as well as the norm of the vector.
aver.xvg contains <|mu|^2> and
|<mu>|^2 during the
dipdist.xvg contains the distribution of dipole moments during
The value of
-mumax is used as the highest value in the distribution graph.
Furthermore, the dipole autocorrelation function will be computed when
-corr is used. The output file name is given with the
The correlation functions can be averaged over all molecules
mol), plotted per molecule separately (
or it can be computed over the total dipole moment of the simulation box
-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
-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)
Portable xdr run input file
-n[<.ndx>] (index.ndx) (Optional)
Options to specify output files:
-c[<.xvg>] (dipcorr.xvg) (Optional)
-g[<.xvg>] (gkr.xvg) (Optional)
-adip[<.xvg>] (adip.xvg) (Optional)
-dip3d[<.xvg>] (dip3d.xvg) (Optional)
-cos[<.xvg>] (cosaver.xvg) (Optional)
-cmap[<.xpm>] (cmap.xpm) (Optional)
X PixMap compatible matrix file
-slab[<.xvg>] (slab.xvg) (Optional)
Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
xvg plot formatting: xmgrace, xmgr, none
dipole of a single molecule (in Debye)
max dipole in Debye (for histogram)
epsilon of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity (default)
Skip steps in the output (but not in the computations)
Average temperature of the simulation (needed for dielectric constant calculation)
Correlation function to calculate: none, mol, molsep, total
Calculate |cos(theta)| between all pairs of molecules. May be slow
Take quadrupole into account
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
Take the normal on the computational box in direction X, Y or Z.
Divide the box into this number of slices.
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
Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules
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
-cmapoption. By default the cosine of the angle between the dipoles is plotted.
Number of colors in the cmap output
Number of divisions on the y-axis in the cmap output (for 180 degrees)
Length of the ACF, default is half the number of frames
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
Time where to begin the exponential fit of the correlation function
Time where to end the exponential fit of the correlation function, -1 is until the end