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g_dipoles - computes the total dipole plus fluctuationsVERSION4.0.1

g_dipoles-enxener.edr-ftraj.xtc-stopol.tpr-nindex.ndx-oMtot.xvg-epsepsilon.xvg-aaver.xvg-ddipdist.xvg-cdipcorr.xvg-ggkr.xvg-adipadip.xvg-dip3ddip3d.xvg-coscosaver.xvg-cmapcmap.xpm-qquadrupole.xvg-slabslab.xvg-[no]h-niceint-btime-etime-dttime-[no]w-[no]xvgr-mureal-mumaxreal-epsilonRFreal-skipint-tempreal-correnum-[no]pairs-ncosint-axisstring-slint-gkratomint-gkratom2int-rcmaxreal-[no]phi-nlevelsint-ndegreesint-acflenint-[no]normalize-Penum-fitfnenum-ncskipint-beginfitreal-endfitreal

g_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 mu_max 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-coption. The correlation functions can be averaged over all molecules (mol), plotted per molecule seperately (molsep) or it can be computed over the total dipole moment of the simulation box (total). Option-gproduces 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, JCP 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 g_dipoles -corr mol -P1 -o dip_sqr -mu 2.273 -mumax 5.0 -nofft 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.

-enxener.edrInput,Opt.Energy file: edr ene-ftraj.xtcInputTrajectory: xtc trr trj gro g96 pdb cpt-stopol.tprInputRun input file: tpr tpb tpa-nindex.ndxInput,Opt.Index file-oMtot.xvgOutputxvgr/xmgr file-epsepsilon.xvgOutputxvgr/xmgr file-aaver.xvgOutputxvgr/xmgr file-ddipdist.xvgOutputxvgr/xmgr file-cdipcorr.xvgOutput,Opt.xvgr/xmgr file-ggkr.xvgOutput,Opt.xvgr/xmgr file-adipadip.xvgOutput,Opt.xvgr/xmgr file-dip3ddip3d.xvgOutput,Opt.xvgr/xmgr file-coscosaver.xvgOutput,Opt.xvgr/xmgr file-cmapcmap.xpmOutput,Opt.X PixMap compatible matrix file-qquadrupole.xvgOutput,Opt.xvgr/xmgr file-slabslab.xvgOutput,Opt.xvgr/xmgr file

-[no]hnoPrint help info and quit-niceint19Set the nicelevel-btime0First frame (ps) to read from trajectory-etime0Last frame (ps) to read from trajectory-dttime0Only use frame when t MOD dt = first time (ps)-[no]wnoView output xvg, xpm, eps and pdb files-[no]xvgryesAdd specific codes (legends etc.) in the output xvg files for the xmgrace program-mureal-1dipole of a single molecule (in Debye)-mumaxreal5max dipole in Debye (for histrogram)-epsilonRFreal0epsilon of the reaction field used during the simulation, needed for dieclectric constant calculation. WARNING: 0.0 means infinity (default)-skipint0Skip steps in the output (but not in the computations)-tempreal300Average temperature of the simulation (needed for dielectric constant calculation)-correnumnoneCorrelation function to calculate:none,mol,molseportotal-[no]pairsyesCalculate |cos theta| between all pairs of molecules. May be slow-ncosint1Must be 1 or 2. Determines whether the cos is computed between all mole cules in one group, or between molecules in two different groups. This turns on the -gkr flag.-axisstringZTake the normal on the computational box in direction X, Y or Z.-slint10Divide the box in nr slices.-gkratomint0Use 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-gkratom2int0Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules-rcmaxreal0Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterium based on the box length will be used.-[no]phinoPlot 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.-nlevelsint20Number of colors in the cmap output-ndegreesint90Number of divisions on the y-axis in the camp output (for 180 degrees)-acflenint-1Length of the ACF, default is half the number of frames-[no]normalizeyesNormalize ACF-Penum0Order of Legendre polynomial for ACF (0 indicates none):0,1,2or3-fitfnenumnoneFit function:none,exp,aexp,exp_exp,vac,exp5,exp7orexp9-ncskipint0Skip N points in the output file of correlation functions-beginfitreal0Time where to begin the exponential fit of the correlation function-endfitreal-1Time where to end the exponential fit of the correlation function, -1 is till the end

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Thu 16 Oct 2008 g_dipoles(1)