.TH gmx-tcaf 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-tcaf \- Calculate viscosities of liquids

.SH SYNOPSIS
gmx tcaf [\-f [<.trr/.cpt/...>]] [\-s [<.tpr/.tpb/...>]] [\-n [<.ndx>]]
         [\-ot [<.xvg>]] [\-oa [<.xvg>]] [\-o [<.xvg>]] [\-of [<.xvg>]]
         [\-oc [<.xvg>]] [\-ov [<.xvg>]] [\-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>] [\-beginfit <real>]
         [\-endfit <real>]

.SH DESCRIPTION
\fBgmx tcaf\fR 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 \fIy\fR\- and \fIz\fR\-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 \fB\-wt\fR) 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 \fB\-oc\fR, 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 \fB\-oc\fR The cubic eta estimates are also written to \fB\-ov\fR.

With option \fB\-mol\fR, 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 \fB\-ov\fR file should be fitted to eta(k) = eta_0 (1 \- a k2) to obtain the viscosity at infinite wavelength.

\fBNote:\fR 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.

.SH OPTIONS
Options to specify input and output files:

.BI "\-f" " [<.trr/.cpt/...>] (traj.trr) (Input)"
    Full precision trajectory: trr cpt trj tng

.BI "\-s" " [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)"
    Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

.BI "\-n" " [<.ndx>] (index.ndx) (Input, Optional)"
    Index file

.BI "\-ot" " [<.xvg>] (transcur.xvg) (Output, Optional)"
    xvgr/xmgr file

.BI "\-oa" " [<.xvg>] (tcaf_all.xvg) (Output)"
    xvgr/xmgr file

.BI "\-o" " [<.xvg>] (tcaf.xvg) (Output)"
    xvgr/xmgr file

.BI "\-of" " [<.xvg>] (tcaf_fit.xvg) (Output)"
    xvgr/xmgr file

.BI "\-oc" " [<.xvg>] (tcaf_cub.xvg) (Output, Optional)"
    xvgr/xmgr file

.BI "\-ov" " [<.xvg>] (visc_k.xvg) (Output)"
    xvgr/xmgr file


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-dt" " <time> (0)"
    Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w" "  (no)"
    View output \fB.xvg\fR, \fB.xpm\fR, \fB.eps\fR and \fB.pdb\fR files

.BI "\-xvg" " <enum> (xmgrace)"
    xvg plot formatting: xmgrace, xmgr, none

.BI "\-[no]mol" "  (no)"
    Calculate TCAF of molecules

.BI "\-[no]k34" "  (no)"
    Also use k=(3,0,0) and k=(4,0,0)

.BI "\-wt" " <real> (5)"
    Exponential decay time for the TCAF fit weights

.BI "\-acflen" " <int> (-1)"
    Length of the ACF, default is half the number of frames

.BI "\-[no]normalize" "  (yes)"
    Normalize ACF

.BI "\-P" " <enum> (0)"
    Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3

.BI "\-fitfn" " <enum> (none)"
    Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9, erffit

.BI "\-beginfit" " <real> (0)"
    Time where to begin the exponential fit of the correlation function

.BI "\-endfit" " <real> (-1)"
    Time where to end the exponential fit of the correlation function, \-1 is until the end


.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.