Provided by: gromacs-data_4.6.5-1build1_all bug


       g_tcaf - calculates viscosities of liquids

       VERSION 4.6.5


       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


        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.


       -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


        Print help info and quit

        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)

        View output  .xvg,  .xpm,  .eps and  .pdb files

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

        Calculate TCAF of molecules

        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

        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



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                                g_tcaf(1)