g_tcaf(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_tcaf(1)
NAME
g_tcaf - calculates viscosities of liquids
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_tcaf -f traj.trr -s topol.tpr -n index.ndx -ot transcur.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg -oc tcaf_cub.xvg -ov visc_k.xvg
-[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]mol -[no]k34 -wt real -acflen int -[no]normalize -P enum
-fitfn enum -ncskip int -beginfit real -endfit real
DESCRIPTION
g_tcaf computes tranverse current autocorrelations. These are used to estimate the shear viscosity, eta. For details see: Palmer, Phys.
Rev. E 49 (1994) pp 359-366.
Transverse currents are calculated using the k-vectors (1,0,0) and (2,0,0) each also in the y- and z-direction, (1,1,0) and (1,-1,0) each
also in the 2 other planes (these vectors are not independent) and (1,1,1) and the 3 other box diagonals (also not independent). For each
k-vector the sine and cosine are used, in combination with the velocity in 2 perpendicular directions. This gives a total of 16*2*2=64
transverse currents. One autocorrelation is calculated fitted for each k-vector, which gives 16 TCAF's. Each of these TCAF's is fitted to
f(t) = exp(-v)(cosh(Wv) + 1/W sinh(Wv)), v = -t/(2 tau), W = sqrt(1 - 4 tau eta/rho k2), which gives 16 values of tau and eta. The fit
weights decay with time as exp(-t/wt), and the TCAF and fit are calculated up to time 5*wt. The eta values should be fitted to 1 - a
eta(k) k2, from which one can estimate the shear viscosity at k=0.
When the box is cubic, one can use the option -oc, which averages the TCAF's over all k-vectors with the same length. This results in
more accurate tcaf's. Both the cubic TCAF's and fits are written to -oc The cubic eta estimates are also written to -ov.
With option -mol, the transverse current is determined of molecules instead of atoms. In this case, the index group should consist of mol-
ecule numbers instead of atom numbers.
The k-dependent viscosities in the -ov file should be fitted to eta(k) = eta0 (1 - a k2) to obtain the viscosity at infinite wavelength.
Note: make sure you write coordinates and velocities often enough. The initial, non-exponential, part of the autocorrelation function is
very important for obtaining a good fit.
FILES
-f traj.trr Input
Full precision trajectory: trr trj cpt
-s topol.tpr Input, Opt.
Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt.
Index file
-ot transcur.xvg Output, Opt.
xvgr/xmgr file
-oa tcaf_all.xvg Output
xvgr/xmgr file
-o tcaf.xvg Output
xvgr/xmgr file
-of tcaf_fit.xvg Output
xvgr/xmgr file
-oc tcaf_cub.xvg Output, Opt.
xvgr/xmgr file
-ov visc_k.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]molno
Calculate tcaf of molecules
-[no]k34no
Also use k=(3,0,0) and k=(4,0,0)
-wt real 5
Exponential decay time for the TCAF fit weights
-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, exp9 or erffit
-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 until the end
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_tcaf(1)