Man page - gmx-tcaf(1)
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apt-get install gromacs-data
Manual
GMX-TCAF
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
NAME
gmx-tcaf - Calculate viscosities of liquids
SYNOPSIS
gmx tcaf
[
-f
[<.trr/.cpt/...>]
] [
-s
[<.tpr/.gro/...>]
] [
-n
[<.ndx>]
]
[
-ot
[<.xvg>]
] [
-oa
[<.xvg>]
] [
-o
[<.xvg>]
]
[
-of
[<.xvg>]
]
[
-oc
[<.xvg>]
] [
-ov
[<.xvg>]
] [
-b
<time>
]
[
-e
<time>
]
[
-dt
<time>
] [
-[no]w
]
[
-xvg
<enum>
] [
-[no]mol
]
[
-[no]k34
]
[
-wt
<real>
] [
-acflen
<int>
] [
-[no]normalize
] [
-P
<enum>
]
[
-fitfn
<enum>
] [
-beginfit
<real>
] [
-endfit
<real>
]
DESCRIPTION
gmx 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 TCAFs. Each of these TCAFs is fitted to f(t) = exp(-v)(cosh(Wv) + 1/W sinh(Wv)), v = -t/(2 tau), W = sqrt(1 - 4 tau eta/rho kĖ2), which gives 16 values of tau and eta. The fit weights decay exponentially with time constant w (given with -wt ) as exp(-t/w), and the TCAF and fit are calculated up to time 5*w. The eta values should be fitted to 1 - a eta(k) kĖ2, 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 TCAFs over all k-vectors with the same length. This results in more accurate TCAFs. Both the cubic TCAFs 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 molecule numbers instead of atom numbers.
The k-dependent viscosities in the -ov file should be fitted to eta(k) = eta_0 (1 - a kĖ2) 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.
OPTIONS
Options to
specify input files:
-f [<.trr/.cpt/...>] (traj.trr)
Full precision trajectory: trr cpt tng
-s [<.tpr/.gro/...>] (topol.tpr) (Optional)
Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Optional)
Index file
Options to
specify output files:
-ot [<.xvg>] (transcur.xvg) (Optional)
xvgr/xmgr file
-oa [<.xvg>] (tcaf_all.xvg)
xvgr/xmgr file
-o [<.xvg>] (tcaf.xvg)
xvgr/xmgr file
-of [<.xvg>] (tcaf_fit.xvg)
xvgr/xmgr file
-oc [<.xvg>] (tcaf_cub.xvg) (Optional)
xvgr/xmgr file
-ov [<.xvg>] (visc_k.xvg)
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)
View output .xvg , .xpm , .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[no]mol (no)
Calculate TCAF of molecules
-[no]k34 (no)
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]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
SEE ALSO
gmx(1)
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2025, GROMACS development team