# gmx tcaf#

## 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)

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