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NAME

       g_tcaf - calculates viscosities of liquids

       VERSION 4.0.1

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  -nice int -b time -e time -dt time -[no]w -[no]xvgr
       -[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,  JCP  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  plains (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 tcaf’s. Each of these tcaf’s 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 tau’s and eta’s. The fit weights decay with
       time  as  exp(-t/wt),  the tcaf and fit are calculated up to time 5*wt.
       The eta’s 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
       tcaf’s over all k-vectors with the same length.  This results  in  more
       accurate  tcaf’s.   Both  the cubic tcaf’s 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)
       = eta0 (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

       -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

       -[no]xvgryes
        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

       -[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 or
       exp9

       -ncskip int 0
        Skip N 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 till the end

SEE ALSO

       gromacs(7)

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

                                Thu 16 Oct 2008                      g_tcaf(1)