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       gmx-tcaf - Calculate viscosities of liquids


          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>]


       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 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 -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 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 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



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