g_tcaf computes tranverse current autocorrelations. These are used to estimate the shear viscosity eta. For details see: Palmer, JCP 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.
|-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|
|-oc||tcaf_cub.xvg||Output, Opt.||xvgr/xmgr file|
|-[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|
|-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|