Provided by: gromacs-data_2018.1-1_all

**NAME**

gmx-tcaf - 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**

gmxtcafcomputes 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 they- andz-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-ocThe 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-ovfile 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

**SEE** **ALSO**

gmx(1)More information about GROMACS is available at <http://www.gromacs.org/>.

**COPYRIGHT**

2018, GROMACS development team