# gmx-tcaf - Man Page

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/ā¦>] (traj.trr)**Full precision trajectory: trr cpt tng

**-s [<.tpr/.gro/ā¦>] (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

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

## Copyright

2020, GROMACS development team