# g_dipoles(1) [debian man page]

g_dipoles(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_dipoles(1)NAME

g_dipoles - computes the total dipole plus fluctuations VERSION 4.5.4-dev-20110404-bc5695cSYNOPSIS

g_dipolesener.edr-entraj.xtc-ftopol.tpr-sindex.ndx-nMtot.xvg-oepsilon.xvg-epsaver.xvg-adipdist.xvg-ddipcorr.xvg-cgkr.xvg-gadip.xvg-adipdip3d.xvg-dip3dcosaver.xvg-coscmap.xpm-cmapquadrupole.xvg-qslab.xvg -[no]h -[no]version-slabint-nicetime-btime-etime -[no]w-dtenum-xvgreal-mureal-mumaxreal-epsilonRFint-skipreal-tempenum -[no]pairs-corrint-ncosstring-axisint-slint-gkratomint-gkratom2real -[no]phi-rcmaxint-nlevelsint-ndegreesint -[no]normalize-acflenenum-Penum-fitfnint-ncskipreal-beginfitreal-endfitDESCRIPTION

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 con- tains |Mu|2 and | Mu |2 during the simulation. The file dipdist.xvg contains the distribution of dipole moments during the simulation The value ofis used as the highest value in the distribution graph. Furthermore, the dipole autocorrelation function will be computed when option-mumaxis used. The output file name is given with the-corroption. The correlation functions can be averaged over all molecules ( mol), plotted per molecule separately ( molsep) or it can be com- puted over the total dipole moment of the simulation box ( total). Option-cproduces 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 g_dipoles-gmol-corr-o dip_sqr-P12.273-mu5.0-mumaxThis 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.-nofftFILES

ener.edr Input, Opt. Energy file-entraj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt-ftopol.tpr Input Run input file: tpr tpb tpa-sindex.ndx Input, Opt. Index file-nMtot.xvg Output xvgr/xmgr file-oepsilon.xvg Output xvgr/xmgr file-epsaver.xvg Output xvgr/xmgr file-adipdist.xvg Output xvgr/xmgr file-ddipcorr.xvg Output, Opt. xvgr/xmgr file-cgkr.xvg Output, Opt. xvgr/xmgr file-gadip.xvg Output, Opt. xvgr/xmgr file-adipdip3d.xvg Output, Opt. xvgr/xmgr file-dip3dcosaver.xvg Output, Opt. xvgr/xmgr file-coscmap.xpm Output, Opt. X PixMap compatible matrix file-cmapquadrupole.xvg Output, Opt. xvgr/xmgr file-qslab.xvg Output, Opt. xvgr/xmgr file-slabOTHER OPTIONS

-[no]hno Print help info and quit -[no]versionno Print version info and quitint 19 Set the nicelevel-nicetime 0 First frame (ps) to read from trajectory-btime 0 Last frame (ps) to read from trajectory-etime 0 Only use frame when t MOD dt = first time (ps) -[no]wno View output .xvg, .xpm, .eps and .pdb files-dtenum xmgrace xvg plot formatting: xmgrace, xmgr or none-xvgreal-mudipole of a single molecule (in Debye)-1real 5 max dipole in Debye (for histrogram)-mumaxreal 0 epsilon of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity (default)-epsilonRFint 0 Skip steps in the output (but not in the computations)-skipreal 300 Average temperature of the simulation (needed for dielectric constant calculation)-tempenum none Correlation function to calculate: none, mol, molsep or total -[no]pairsyes Calculate |cos theta| between all pairs of molecules. May be slow-corrint 1 Must be 1 or 2. Determines whether the cos is computed between all molecules in one group, or between molecules in two different groups. This turns on the-ncosflag.-gkrstring Z Take the normal on the computational box in direction X, Y or Z.-axisint 10 Divide the box in nr slices.-slint 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-gkratomint 0 Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules-gkratom2real 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]phino 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-rcmaxoption. By default the cosine of the angle between the dipoles is plotted.-cmapint 20 Number of colors in the cmap output-nlevelsint 90 Number of divisions on the y-axis in the cmap output (for 180 degrees)-ndegreesint-acflenLength of the ACF, default is half the number of frames -[no]normalizeyes Normalize ACF-1enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3-Penum none Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit-fitfnint 0 Skip N points in the output file of correlation functions-ncskipreal 0 Time where to begin the exponential fit of the correlation function-beginfitreal-endfitTime where to end the exponential fit of the correlation function,-1is until the end-1SEE ALSO

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_dipoles(1)