1GMX-TCAF(1)                         GROMACS                        GMX-TCAF(1)
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NAME

6       gmx-tcaf - Calculate viscosities of liquids
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SYNOPSIS

9          gmx tcaf [-f [<.trr/.cpt/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                   [-ot [<.xvg>]] [-oa [<.xvg>]] [-o [<.xvg>]] [-of [<.xvg>]]
11                   [-oc [<.xvg>]] [-ov [<.xvg>]] [-b <time>] [-e <time>]
12                   [-dt <time>] [-[no]w] [-xvg <enum>] [-[no]mol] [-[no]k34]
13                   [-wt <real>] [-acflen <int>] [-[no]normalize] [-P <enum>]
14                   [-fitfn <enum>] [-beginfit <real>] [-endfit <real>]
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DESCRIPTION

17       gmx  tcaf  computes tranverse current autocorrelations.  These are used
18       to estimate the shear viscosity, eta.  For details see:  Palmer,  Phys.
19       Rev. E 49 (1994) pp 359-366.
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21       Transverse  currents  are  calculated  using  the k-vectors (1,0,0) and
22       (2,0,0) each also in the y- and z-direction, (1,1,0) and (1,-1,0)  each
23       also  in  the  2  other  planes (these vectors are not independent) and
24       (1,1,1) and the 3 other box diagonals (also not independent). For  each
25       k-vector the sine and cosine are used, in combination with the velocity
26       in 2 perpendicular directions. This gives a total of  16*2*2=64  trans‐
27       verse  currents.  One  autocorrelation  is  calculated  fitted for each
28       k-vector, which gives 16 TCAFs. Each of these TCAFs is fitted to f(t) =
29       exp(-v)(cosh(Wv)  +  1/W  sinh(Wv)), v = -t/(2 tau), W = sqrt(1 - 4 tau
30       eta/rho k^2), which gives 16 values of tau and  eta.  The  fit  weights
31       decay exponentially with time constant w (given with -wt) as exp(-t/w),
32       and the TCAF and fit are calculated up to time  5*w.   The  eta  values
33       should  be  fitted to 1 - a eta(k) k^2, from which one can estimate the
34       shear viscosity at k=0.
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36       When the box is cubic, one can use the option -oc, which  averages  the
37       TCAFs  over  all  k-vectors with the same length.  This results in more
38       accurate TCAFs.  Both the cubic TCAFs and fits are written to  -oc  The
39       cubic eta estimates are also written to -ov.
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41       With  option  -mol,  the  transverse current is determined of molecules
42       instead of atoms. In this case, the index group should consist of mole‐
43       cule numbers instead of atom numbers.
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45       The  k-dependent viscosities in the -ov file should be fitted to eta(k)
46       = eta_0 (1 - a k^2) to obtain the viscosity at infinite wavelength.
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48       Note: make sure you write coordinates and velocities often enough.  The
49       initial,  non-exponential, part of the autocorrelation function is very
50       important for obtaining a good fit.
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OPTIONS

53       Options to specify input files:
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55       -f [<.trr/.cpt/…>] (traj.trr)
56              Full precision trajectory: trr cpt tng
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58       -s [<.tpr/.gro/…>] (topol.tpr) (Optional)
59              Structure+mass(db): tpr gro g96 pdb brk ent
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61       -n [<.ndx>] (index.ndx) (Optional)
62              Index file
63
64       Options to specify output files:
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66       -ot [<.xvg>] (transcur.xvg) (Optional)
67              xvgr/xmgr file
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69       -oa [<.xvg>] (tcaf_all.xvg)
70              xvgr/xmgr file
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72       -o [<.xvg>] (tcaf.xvg)
73              xvgr/xmgr file
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75       -of [<.xvg>] (tcaf_fit.xvg)
76              xvgr/xmgr file
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78       -oc [<.xvg>] (tcaf_cub.xvg) (Optional)
79              xvgr/xmgr file
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81       -ov [<.xvg>] (visc_k.xvg)
82              xvgr/xmgr file
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84       Other options:
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86       -b <time> (0)
87              Time of first frame to read from trajectory (default unit ps)
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89       -e <time> (0)
90              Time of last frame to read from trajectory (default unit ps)
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92       -dt <time> (0)
93              Only use frame when t MOD dt = first time (default unit ps)
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95       -[no]w (no)
96              View output .xvg, .xpm, .eps and .pdb files
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98       -xvg <enum> (xmgrace)
99              xvg plot formatting: xmgrace, xmgr, none
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101       -[no]mol (no)
102              Calculate TCAF of molecules
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104       -[no]k34 (no)
105              Also use k=(3,0,0) and k=(4,0,0)
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107       -wt <real> (5)
108              Exponential decay time for the TCAF fit weights
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110       -acflen <int> (-1)
111              Length of the ACF, default is half the number of frames
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113       -[no]normalize (yes)
114              Normalize ACF
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116       -P <enum> (0)
117              Order of Legendre polynomial for ACF (0 indicates none):  0,  1,
118              2, 3
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120       -fitfn <enum> (none)
121              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
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123       -beginfit <real> (0)
124              Time where to begin the exponential fit of the correlation func‐
125              tion
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127       -endfit <real> (-1)
128              Time where to end the exponential fit of the  correlation  func‐
129              tion, -1 is until the end
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SEE ALSO

132       gmx(1)
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134       More     information    about    GROMACS    is    available    at    <‐
135       http://www.gromacs.org/>.
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138       2019, GROMACS development team
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1432019.4                           Oct 02, 2019                      GMX-TCAF(1)
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