.. _gmx dipoles: gmx dipoles =========== Synopsis -------- .. parsed-literal:: gmx dipoles [:strong:`-en` :emphasis:`[<.edr>]`] [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr>]`] [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-o` :emphasis:`[<.xvg>]`] [:strong:`-eps` :emphasis:`[<.xvg>]`] [:strong:`-a` :emphasis:`[<.xvg>]`] [:strong:`-d` :emphasis:`[<.xvg>]`] [:strong:`-c` :emphasis:`[<.xvg>]`] [:strong:`-g` :emphasis:`[<.xvg>]`] [:strong:`-adip` :emphasis:`[<.xvg>]`] [:strong:`-dip3d` :emphasis:`[<.xvg>]`] [:strong:`-cos` :emphasis:`[<.xvg>]`] [:strong:`-cmap` :emphasis:`[<.xpm>]`] [:strong:`-slab` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`] [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-mu` :emphasis:`<real>`] [:strong:`-mumax` :emphasis:`<real>`] [:strong:`-epsilonRF` :emphasis:`<real>`] [:strong:`-skip` :emphasis:`<int>`] [:strong:`-temp` :emphasis:`<real>`] [:strong:`-corr` :emphasis:`<enum>`] [:strong:`-[no]pairs`] [:strong:`-[no]quad`] [:strong:`-ncos` :emphasis:`<int>`] [:strong:`-axis` :emphasis:`<string>`] [:strong:`-sl` :emphasis:`<int>`] [:strong:`-gkratom` :emphasis:`<int>`] [:strong:`-gkratom2` :emphasis:`<int>`] [:strong:`-rcmax` :emphasis:`<real>`] [:strong:`-[no]phi`] [:strong:`-nlevels` :emphasis:`<int>`] [:strong:`-ndegrees` :emphasis:`<int>`] [:strong:`-acflen` :emphasis:`<int>`] [:strong:`-[no]normalize`] [:strong:`-P` :emphasis:`<enum>`] [:strong:`-fitfn` :emphasis:`<enum>`] [:strong:`-beginfit` :emphasis:`<real>`] [:strong:`-endfit` :emphasis:`<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\|^2> and \|<mu>\|^2 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: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`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 :ref:`.xvg <xvg>`, :ref:`.xpm <xpm>`, :ref:`.eps <eps>` and :ref:`.pdb <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 :ref:`.xpm <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 .. only:: man See also -------- :manpage:`gmx(1)` More information about |Gromacs| is available at <http://www.gromacs.org/>.