NAME

       g_tcaf - calculates viscosities of liquids

       VERSION 4.6.5

SYNOPSIS

       g_tcaf  -f  traj.trr  -s  topol.tpr  -n  index.ndx  -ot  transcur.xvg  -oa  tcaf_all.xvg  -o tcaf.xvg -of
       tcaf_fit.xvg -oc tcaf_cub.xvg -ov visc_k.xvg -[no]h -[no]version -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 -ncskip int
       -beginfit real -endfit real

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 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.

FILES

       -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

       -[no]hno
        Print help info and quit

       -[no]versionno
        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]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -[no]molno
        Calculate TCAF of molecules

       -[no]k34no
        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]normalizeyes
        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,  exp9 or  erffit

       -ncskip int 0
        Skip this many 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

SEE ALSO

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                        g_tcaf(1)