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       g_tcaf - calculates viscosities of liquids

       VERSION 4.0.1


       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


       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.


       -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

       -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

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

        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

       -fitfn enum none
        Fit  function:   none,   exp,   aexp,   exp_exp,  vac,  exp5,  exp7 or

       -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



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                      g_tcaf(1)