**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 k2), 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) 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 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 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.

Options to specify input and output files:
**-f*** [<.trr/.cpt/...>] (traj.trr) (Input)*

Full precision trajectory: trr cpt trj tng

**-s*** [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)*

Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

**-n*** [<.ndx>] (index.ndx) (Input, Optional)*

Index file

**-ot*** [<.xvg>] (transcur.xvg) (Output, Optional)*

xvgr/xmgr file

**-oa*** [<.xvg>] (tcaf_all.xvg) (Output)*

xvgr/xmgr file

**-o*** [<.xvg>] (tcaf.xvg) (Output)*

xvgr/xmgr file

**-of*** [<.xvg>] (tcaf_fit.xvg) (Output)*

xvgr/xmgr file

**-oc*** [<.xvg>] (tcaf_cub.xvg) (Output, Optional)*

xvgr/xmgr file

**-ov*** [<.xvg>] (visc_k.xvg) (Output)*

xvgr/xmgr file

Other options:

**-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]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, vac, exp5, exp7, exp9, erffit

**-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