g_tcaf

| ## g_tcaf Main Table of Contents | VERSION 4.5 Thu 26 Aug 2010

### Description

g_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 tcaf's. Each of these tcaf's 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 tau's and eta's. The fit weights decay with time as exp(-t/wt), the tcaf and fit are calculated up to time 5*wt. The eta's 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 tcaf's over all k-vectors with the same length. This results in more accurate tcaf's. Both the cubic tcaf's 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) = eta0 (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.

### Files

option | filename | type | description
--- | --- | --- | ---
`-f` | `traj.trr` | Input | Full precision trajectory: trr trj cpt
`-s` | `topol.tpr` | Input, Opt. | Structure+mass(db): tpr tpb tpa gro g96 pdb
`-n` | `index.ndx` | Input, Opt. | Index file
`-ot` | `transcur.xvg` | Output, Opt. | xvgr/xmgr file
`-oa` | `tcaf_all.xvg` | Output | xvgr/xmgr file
`-o` | `tcaf.xvg` | Output | xvgr/xmgr file
`-of` | `tcaf_fit.xvg` | Output | xvgr/xmgr file
`-oc` | `tcaf_cub.xvg` | Output, Opt. | xvgr/xmgr file
`-ov` | `visc_k.xvg` | Output | xvgr/xmgr file

### Other options

option | type | default | description
--- | --- | --- | ---
`-[no]h` | gmx_bool | `no` | Print help info and quit
`-[no]version` | gmx_bool | `no` | Print version info and quit
`-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` | gmx_bool | `no` | View output xvg, xpm, eps and pdb files
`-xvg` | enum | `xmgrace` | xvg plot formatting: `xmgrace`, `xmgr` or `none`
`-[no]mol` | gmx_bool | `no` | Calculate tcaf of molecules
`-[no]k34` | gmx_bool | `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` | gmx_bool | `yes` | Normalize ACF
`-P` | enum | `0` | Order of Legendre polynomial for ACF (0 indicates none): `0`, `1`, `2` or `3`
`-fitfn` | enum | `none` | Fit function: `none`, `exp`, `aexp`, `exp_exp`, `vac`, `exp5`, `exp7` or `exp9`
`-ncskip` | int | `0` | Skip N points in the output file of correlation functions
`-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

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