g_sigeps(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_sigeps(1)NAME
g_sigeps - convert c6/12 or c6/cn combinations to and from sigma/epsilon
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_sigeps -o potje.xvg -[no]h -[no]version -nice int -[no]w -xvg enum -c6 real -cn real -pow int -sig real -eps real -A real -B real -C real
-qi real -qj real -sigfac real
DESCRIPTION
g_sigeps is a simple utility that converts C6/C12 or C6/Cn combinations to sigma and epsilon, or vice versa. It can also plot the poten-
tial in file. In addition, it makes an approximation of a Buckingham potential to a Lennard-Jones potential.
FILES -o potje.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-c6 real 0.001
c6
-cn real 1e-06
constant for repulsion
-pow int 12
power of the repulsion term
-sig real 0.3
sig
-eps real 1
eps
-A real 100000
Buckingham A
-B real 32
Buckingham B
-C real 0.001
Buckingham C
-qi real 0
qi
-qj real 0
qj
-sigfac real 0.7
Factor in front of sigma for starting the plot
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_sigeps(1)
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g_dielectric(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_dielectric(1)NAME
g_dielectric - calculates frequency dependent dielectric constants
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_dielectric -f dipcorr.xvg -d deriv.xvg -o epsw.xvg -c cole.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum
-[no]fft -[no]x1 -eint real -bfit real -efit real -tail real -A real -tau1 real -tau2 real -eps0 real -epsRF real -fix int -ffn enum
-nsmooth int
DESCRIPTION
g_dielectric calculates frequency dependent dielectric constants from the autocorrelation function of the total dipole moment in your sim-
ulation. This ACF can be generated by g_dipoles. For an estimate of the error you can run g_statistics on the ACF, and use the output
thus generated for this program. The functional forms of the available functions are:
One parameter: y = Exp[-a1 x],
Two parameters: y = a2 Exp[-a1 x],
Three parameters: y = a2 Exp[-a1 x] + (1 - a2) Exp[-a3 x].
Start values for the fit procedure can be given on the command line. It is also possible to fix parameters at their start value, use -fix
with the number of the parameter you want to fix.
Three output files are generated, the first contains the ACF, an exponential fit to it with 1, 2 or 3 parameters, and the numerical deriva-
tive of the combination data/fit. The second file contains the real and imaginary parts of the frequency-dependent dielectric constant,
the last gives a plot known as the Cole-Cole plot, in which the imaginary component is plotted as a function of the real component. For a
pure exponential relaxation (Debye relaxation) the latter plot should be one half of a circle.
FILES -f dipcorr.xvg Input
xvgr/xmgr file
-d deriv.xvg Output
xvgr/xmgr file
-o epsw.xvg Output
xvgr/xmgr file
-c cole.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version 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
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-[no]fftno
use fast fourier transform for correlation function
-[no]x1yes
use first column as x-axis rather than first data set
-eint real 5
Time to end the integration of the data and start to use the fit
-bfit real 5
Begin time of fit
-efit real 500
End time of fit
-tail real 500
Length of function including data and tail from fit
-A real 0.5
Start value for fit parameter A
-tau1 real 10
Start value for fit parameter tau1
-tau2 real 1
Start value for fit parameter tau2
-eps0 real 80
epsilon0 of your liquid
-epsRF real 78.5
epsilon of the reaction field used in your simulation. A value of 0 means infinity.
-fix int 0
Fix parameters at their start values, A (2), tau1 (1), or tau2 (4)
-ffn enum none
Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit
-nsmooth int 3
Number of points for smoothing
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_dielectric(1)