# gmx-tcaf man page

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 k^2), 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) k^2, 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 k^2) 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)**- 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]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)

More information about GROMACS is available at <http://www.gromacs.org/>.

## Copyright

2016, GROMACS development team