g_dipoles(1)

NAME
g_dipoles VERSION 3.2.0

SYNOPSIS
g_dipoles -enx ener.edr -f traj.xtc -s topol.tpr -n index.ndx -o Mtot.xvg -eps epsilon.xvg -a aver.xvg -d dipdist.xvg -c dipcorr.xvg -g gkr.xvg -q quadrupole.xvg -[no]h -nice int -b time -e time -dt time -[no]w -mu real -mumax real -epsilonRF real -skip int -temp real -[no]avercorr -gkratom int -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real

DESCRIPTION
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 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 -c is used. It can be averaged over all molecules, or (with option -avercorr) it can be computed as the autocorrelation of the total dipole moment of the simulation box. At the moment the dielectric constant is calculated only correct if a rectangular or cubic simulation box is used. 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, 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 -P1 -n mols -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.

FILES
-enx ener.edr Input, Opt.
 Generic energy: edr ene -f traj.xtc Input
 Generic trajectory: xtc trr trj gro g96 pdb -s topol.tpr Input
 Generic run input: tpr tpb tpa xml -n index.ndx Input, Opt.
 Index file -o Mtot.xvg Output
 xvgr/xmgr file -eps epsilon.xvg Output
 xvgr/xmgr file -a aver.xvg Output
 xvgr/xmgr file -d dipdist.xvg Output
 xvgr/xmgr file -c dipcorr.xvg Output, Opt.
 xvgr/xmgr file -g gkr.xvg Output, Opt.
 xvgr/xmgr file -q quadrupole.xvg Output, Opt.
 xvgr/xmgr file

OTHER OPTIONS
-[no]h no
 Print help info and quit -nice int 19
 Set the nicelevel -b time -1
 First frame (ps) to read from trajectory -e time -1
 Last frame (ps) to read from trajectory -dt time -1
 Only use frame when t MOD dt = first time (ps) -[no]w no
 View output xvg, xpm, eps and pdb files -mu real -1
 dipole of a single molecule (in Debye) -mumax real 5
 max dipole in Debye (for histrogram) -epsilonRF real 0
 epsilon of the reaction field used during the simulation, needed for dieclectric 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) -[no]avercorr no
 calculate AC function of average dipole moment of the simulation box rather than average of AC function per molecule -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 -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 or 3 -fitfn enum none
 Fit function: none , exp , aexp , exp_exp , vac , exp5 , exp7 or exp9 -ncskip int 0
 Skip N points in the output file of correlation functions -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 till the end