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 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 to specify input files:
Options to specify output files:
Other options: