gmx dipoles#
Synopsis#
gmx dipoles [-en [<.edr>]] [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]] [-o [<.xvg>]] [-eps [<.xvg>]] [-a [<.xvg>]] [-d [<.xvg>]] [-c [<.xvg>]] [-g [<.xvg>]] [-adip [<.xvg>]] [-dip3d [<.xvg>]] [-cos [<.xvg>]] [-cmap [<.xpm>]] [-slab [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>] [-mu <real>] [-mumax <real>] [-epsilonRF <real>] [-skip <int>] [-temp <real>] [-corr <enum>] [-[no]pairs] [-[no]quad] [-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>] [-beginfit <real>] [-endfit <real>]
Description#
gmx 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 value of -mumax
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 separately (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, 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
gmx dipoles -corr mol -P 1 -o dip_sqr -mu 2.273 -mumax 5.0
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.
Options#
Options to specify input files:
-en
[<.edr>] (ener.edr) (Optional)Energy file
-f
[<.xtc/.trr/…>] (traj.xtc)-s
[<.tpr>] (topol.tpr)Portable xdr run input file
-n
[<.ndx>] (index.ndx) (Optional)Index file
Options to specify output files:
-o
[<.xvg>] (Mtot.xvg)xvgr/xmgr file
-eps
[<.xvg>] (epsilon.xvg)xvgr/xmgr file
-a
[<.xvg>] (aver.xvg)xvgr/xmgr file
-d
[<.xvg>] (dipdist.xvg)xvgr/xmgr file
-c
[<.xvg>] (dipcorr.xvg) (Optional)xvgr/xmgr file
-g
[<.xvg>] (gkr.xvg) (Optional)xvgr/xmgr file
-adip
[<.xvg>] (adip.xvg) (Optional)xvgr/xmgr file
-dip3d
[<.xvg>] (dip3d.xvg) (Optional)xvgr/xmgr file
-cos
[<.xvg>] (cosaver.xvg) (Optional)xvgr/xmgr file
-cmap
[<.xpm>] (cmap.xpm) (Optional)X PixMap compatible matrix file
-slab
[<.xvg>] (slab.xvg) (Optional)xvgr/xmgr file
Other options:
-b
<time> (0)Time of first frame to read from trajectory (default unit ps)
-e
<time> (0)Time of last frame to read from trajectory (default unit ps)
-dt
<time> (0)Only use frame when t MOD dt = first time (default unit ps)
-[no]w
(no)-xvg
<enum> (xmgrace)xvg plot formatting: xmgrace, xmgr, none
-mu
<real> (-1)dipole of a single molecule (in Debye)
-mumax
<real> (5)max dipole in Debye (for histogram)
-epsilonRF
<real> (0)epsilon of the reaction field used during the simulation, needed for dielectric 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, total
-[no]pairs
(yes)Calculate |cos(theta)| between all pairs of molecules. May be slow
-[no]quad
(no)Take quadrupole into account
-ncos
<int> (1)Must be 1 or 2. Determines whether the <cos(theta)> is computed between all molecules in one group, or between molecules in two different groups. This turns on the
-g
flag.-axis
<string> (Z)Take the normal on the computational box in direction X, Y or Z.
-sl
<int> (10)Divide the box into this number of 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 criterion based on the box length will be used.
-[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 .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 cmap output (for 180 degrees)
-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, 3
-fitfn
<enum> (none)Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
-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 until the end