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g_dipoles_d

NAME

g_dipoles - computes the total dipole plus fluctuations

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

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.