.TH g_dipoles 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_dipoles - computes the total dipole plus fluctuations .B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_dipoles\fP .BI "\-en" " ener.edr " .BI "\-f" " traj.xtc " .BI "\-s" " topol.tpr " .BI "\-n" " index.ndx " .BI "\-o" " Mtot.xvg " .BI "\-eps" " epsilon.xvg " .BI "\-a" " aver.xvg " .BI "\-d" " dipdist.xvg " .BI "\-c" " dipcorr.xvg " .BI "\-g" " gkr.xvg " .BI "\-adip" " adip.xvg " .BI "\-dip3d" " dip3d.xvg " .BI "\-cos" " cosaver.xvg " .BI "\-cmap" " cmap.xpm " .BI "\-q" " quadrupole.xvg " .BI "\-slab" " slab.xvg " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-b" " time " .BI "\-e" " time " .BI "\-dt" " time " .BI "\-[no]w" "" .BI "\-xvg" " enum " .BI "\-mu" " real " .BI "\-mumax" " real " .BI "\-epsilonRF" " real " .BI "\-skip" " int " .BI "\-temp" " real " .BI "\-corr" " enum " .BI "\-[no]pairs" "" .BI "\-ncos" " int " .BI "\-axis" " string " .BI "\-sl" " int " .BI "\-gkratom" " int " .BI "\-gkratom2" " int " .BI "\-rcmax" " real " .BI "\-[no]phi" "" .BI "\-nlevels" " int " .BI "\-ndegrees" " int " .BI "\-acflen" " int " .BI "\-[no]normalize" "" .BI "\-P" " enum " .BI "\-fitfn" " enum " .BI "\-ncskip" " int " .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION \&\fB g_dipoles\fR 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 \¢er of mass of the molecule. \&The file \fB Mtot.xvg\fR contains the total dipole moment of a frame, the \&components as well as the norm of the vector. \&The file \fB aver.xvg\fR contains |Mu|2 and | Mu |2 during the \&simulation. \&The file \fB dipdist.xvg\fR contains the distribution of dipole moments during \&the simulation \&The value of \fB \-mumax\fR is used as the highest value in the distribution graph. \&Furthermore, the dipole autocorrelation function will be computed when \&option \fB \-corr\fR is used. The output file name is given with the \fB \-c\fR \&option. \&The correlation functions can be averaged over all molecules \&(\fB mol\fR), plotted per molecule separately (\fB molsep\fR) \&or it can be computed over the total dipole moment of the simulation box \&(\fB total\fR). \&Option \fB \-g\fR 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 \&\fB g_dipoles \-corr mol \-P1 \-o dip_sqr \-mu 2.273 \-mumax 5.0 \-nofft\fR \&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. .SH FILES .BI "\-en" " ener.edr" .B Input, Opt. Energy file .BI "\-f" " traj.xtc" .B Input Trajectory: xtc trr trj gro g96 pdb cpt .BI "\-s" " topol.tpr" .B Input Run input file: tpr tpb tpa .BI "\-n" " index.ndx" .B Input, Opt. Index file .BI "\-o" " Mtot.xvg" .B Output xvgr/xmgr file .BI "\-eps" " epsilon.xvg" .B Output xvgr/xmgr file .BI "\-a" " aver.xvg" .B Output xvgr/xmgr file .BI "\-d" " dipdist.xvg" .B Output xvgr/xmgr file .BI "\-c" " dipcorr.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-g" " gkr.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-adip" " adip.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-dip3d" " dip3d.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-cos" " cosaver.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-cmap" " cmap.xpm" .B Output, Opt. X PixMap compatible matrix file .BI "\-q" " quadrupole.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-slab" " slab.xvg" .B Output, Opt. xvgr/xmgr file .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 19" Set the nicelevel .BI "\-b" " time" " 0 " First frame (ps) to read from trajectory .BI "\-e" " time" " 0 " Last frame (ps) to read from trajectory .BI "\-dt" " time" " 0 " Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR .BI "\-mu" " real" " \-1 " dipole of a single molecule (in Debye) .BI "\-mumax" " real" " 5 " max dipole in Debye (for histrogram) .BI "\-epsilonRF" " real" " 0 " epsilon of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity (default) .BI "\-skip" " int" " 0" Skip steps in the output (but not in the computations) .BI "\-temp" " real" " 300 " Average temperature of the simulation (needed for dielectric constant calculation) .BI "\-corr" " enum" " none" Correlation function to calculate: \fB none\fR, \fB mol\fR, \fB molsep\fR or \fB total\fR .BI "\-[no]pairs" "yes " Calculate |cos theta| between all pairs of molecules. May be slow .BI "\-ncos" " int" " 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 \fB \-gkr\fR flag. .BI "\-axis" " string" " Z" Take the normal on the computational box in direction X, Y or Z. .BI "\-sl" " int" " 10" Divide the box in nr slices. .BI "\-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 .BI "\-gkratom2" " int" " 0" Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules .BI "\-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. .BI "\-[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 \fB .xpm\fR file from the \fB \-cmap\fR option. By default the cosine of the angle between the dipoles is plotted. .BI "\-nlevels" " int" " 20" Number of colors in the cmap output .BI "\-ndegrees" " int" " 90" Number of divisions on the \fI y\fR\-axis in the cmap output (for 180 degrees) .BI "\-acflen" " int" " \-1" Length of the ACF, default is half the number of frames .BI "\-[no]normalize" "yes " Normalize ACF .BI "\-P" " enum" " 0" Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions .BI "\-beginfit" " real" " 0 " Time where to begin the exponential fit of the correlation function .BI "\-endfit" " real" " \-1 " Time where to end the exponential fit of the correlation function, \-1 is until the end .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.