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gmx-tcaf(1)                     GROMACS Manual                     gmx-tcaf(1)

NAME
       gmx-tcaf - Calculate viscosities of liquids

SYNOPSIS
       gmx tcaf [-f [<.trr/.cpt/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
                [-ot [<.xvg>]] [-oa [<.xvg>]] [-o [<.xvg>]] [-of [<.xvg>]]
                [-oc [<.xvg>]] [-ov [<.xvg>]] [-nice <int>] [-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 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
       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

SEE ALSO
       gromacs(7)

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

VERSION 5.0.6                                                      gmx-tcaf(1)