g_dipoles (1) - Linux Manuals

g_dipoles: computes the total dipole plus fluctuations

NAME

g_dipoles - computes the total dipole plus fluctuations

VERSION 4.0.1

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 -cmap cmap.xpm -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 -corr enum -[no]pairs -ncos int -axis string -sl int -gkratom int -gkratom2 int -rcmax real -[no]phi -nlevels int -ndegrees 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. 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 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 -corr is used. The output file name is given with the -c option. The correlation functions can be averaged over all molecules ( mol), plotted per molecule seperately ( molsep) or it can be computed over the total dipole moment of the simulation box ( total).

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 -corr mol -P1 -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.
 Energy file: edr ene 

-f traj.xtc Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

-s topol.tpr Input
 Run input file: tpr tpb tpa 

-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 

-cmap cmap.xpm Output, Opt.
 X PixMap compatible matrix file 

-q quadrupole.xvg Output, Opt.
 xvgr/xmgr file 

-slab slab.xvg Output, Opt.
 xvgr/xmgr file 

OTHER OPTIONS

-[no]hno
 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]wno
 View output xvg, xpm, eps and pdb files

-[no]xvgryes
 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)

-corr enum none
 Correlation function to calculate:  none,  mol,  molsep or  total

-[no]pairsyes
 Calculate |cos theta| between all pairs of molecules. May be slow

-ncos int 1
 Must be 1 or 2. Determines whether the cos is computed between all mole cules in one group, or between molecules in two different groups. This turns on the -gkr flag.

-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

-gkratom2 int 0
 Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules

-rcmax real 0
 Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterium 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 -cmap option. By default the cosine of the angle between the dipoles is plotted.

-nlevels int 20
 Number of colors in the cmap output

-ndegrees int 90
 Number of divisions on the y-axis in the camp output (for 180 degrees)

-acflen int -1
 Length of the ACF, default is half the number of frames

-[no]normalizeyes
 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