man g_dipoles (Commandes) - g_dipoles VERSION 3.3_beta_20050823
NAME
g_dipoles VERSION 3.3_beta_20050823
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 -adip adip.xvg -dip3d dip3d.xvg -cos cosaver.xvg -q quadrupole.xvg -slab slab.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -mu real -mumax real -epsilonRF real -skip int -temp real -[no]avercorr -[no]pairs -axis string -sl int -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
-adip adip.xvg Output, Opt. xvgr/xmgr file
-dip3d dip3d.xvg Output, Opt. xvgr/xmgr file
-cos cosaver.xvg Output, Opt. xvgr/xmgr file
-q quadrupole.xvg Output, Opt. xvgr/xmgr file
-slab slab.xvg Output, Opt. xvgr/xmgr file
OTHER OPTIONS
-[no]h no Print help info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w no View output xvg, xpm, eps and pdb files
-[no]xvgr yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-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
-[no]pairs yes Calculate |cos theta| between all pairs of molecules. May be slow
-axis string Z Take the normal on the computational box in direction X, Y or Z.
-sl int 10 Divide the box in nr slices.
-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