Man page - gmx-dipoles(1)
Packages contains this manual
- gmx-trjorder(1)
- gmx-wheel(1)
- gmx-genion(1)
- gmx-energy(1)
- gmx-rmsdist(1)
- gmx-sham(1)
- gmx-helixorient(1)
- gmx-select(1)
- gmx-nmeig(1)
- gmx-density(1)
- gmx-genrestr(1)
- gmx-bar(1)
- gmx-lie(1)
- gmx-filter(1)
- gmx-scattering(1)
- gmx-anaeig(1)
- gmx-covar(1)
- gmx_d(1)
- gmx-genconf(1)
- gmx-mdrun(1)
- gmx-velacc(1)
- gmx-tcaf(1)
- gmx-insert-molecules(1)
- gmx-bundle(1)
- gmx-hydorder(1)
- gmx-editconf(1)
- gmx-msd(1)
- gmx-confrms(1)
- gmx-cluster(1)
- gmx-saltbr(1)
- gmx-potential(1)
- gmx-current(1)
- gmx-freevolume(1)
- gmx-make_ndx(1)
- gmx-enemat(1)
- gmx(1)
- gmx-gyrate(1)
- gmx-solvate(1)
- gmx-densmap(1)
- gmx-rotacf(1)
- gmx-helix(1)
- gmx_mpi(1)
- gmx-convert-tpr(1)
- gmx-convert-trj(1)
- gmx-polystat(1)
- gmx-angle(1)
- gmx-xpm2ps(1)
- gmx-pdb2gmx(1)
- gmx-sasa(1)
- gmx-x2top(1)
- gmx-trjcat(1)
- gmx-h2order(1)
- gmx-nmr(1)
- gmx-dump(1)
- gmx-spol(1)
- gmx-distance(1)
- gmx-clustsize(1)
- gmx-rama(1)
- gmx-chi(1)
- gmx-pme_error(1)
- gmx-order(1)
- gmx-gangle(1)
- gmx-eneconv(1)
- gmx-tune_pme(1)
- gmx-grompp(1)
- gmx-make_edi(1)
- gmx-trajectory(1)
- gmx-dipoles(1)
- gmx-awh(1)
- gmx-nonbonded-benchmark(1)
- gmx-analyze(1)
- demux(1)
- gmx-disre(1)
- gmx-saxs-legacy(1)
- gmx-sigeps(1)
- gmx-mdmat(1)
- xplor2gmx(1)
- gmx-check(1)
- gmx-vanhove(1)
- gmx-dssp(1)
- gmx-densorder(1)
- gmx-principal(1)
- gmx-mindist(1)
- gmx-spatial(1)
- gmx-wham(1)
- gmx-rmsf(1)
- gmx-dos(1)
- gmx-mk_angndx(1)
- gmx-nmens(1)
- gmx-dielectric(1)
- gmx-sorient(1)
- gmx-help(1)
- gmx-hbond-legacy(1)
- gmx-sans-legacy(1)
- gmx-gyrate-legacy(1)
- gmx-hbond(1)
- gmx-rotmat(1)
- gmx-extract-cluster(1)
- gmx-rms(1)
- gmx-dyecoupl(1)
- gmx-rdf(1)
- gmx-pairdist(1)
- gmx-trjconv(1)
- gmx-traj(1)
- gmx_mpi_d(1)
- gmx-report-methods(1)
- gmx-nmtraj(1)
apt-get install gromacs-data
Manual
GMX-DIPOLES
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
NAME
gmx-dipoles - Compute the total dipole plus fluctuations
SYNOPSIS
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>
]
DESCRIPTION
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|ˆ2> and |<mu>|ˆ2 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.
EXAMPLES
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
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 end
SEE ALSO
gmx(1)
More information about GROMACS is available at <- http://www.gromacs.org/ >.
COPYRIGHT
2025, GROMACS development team