g_tcaf(1)

1g_tcaf(1)                 GROMACS suite, VERSION 4.5                 g_tcaf(1)
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NAME

6       g_tcaf - calculates viscosities of liquids
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8       VERSION 4.5
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SYNOPSIS

11       g_tcaf  -f  traj.trr  -s  topol.tpr  -n  index.ndx -ot transcur.xvg -oa
12       tcaf_all.xvg  -o  tcaf.xvg  -of  tcaf_fit.xvg  -oc   tcaf_cub.xvg   -ov
13       visc_k.xvg  -[no]h  -[no]version  -nice  int  -b  time -e time -dt time
14       -[no]w -xvg enum -[no]mol -[no]k34 -wt real -acflen int  -[no]normalize
15       -P enum -fitfn enum -ncskip int -beginfit real -endfit real
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DESCRIPTION

18       g_tcaf  computes tranverse current autocorrelations.  These are used to
19       estimate the shear viscosity eta.  For  details  see:  Palmer,  JCP  49
20       (1994) pp 359-366.
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23       Transverse  currents  are  calculated  using  the k-vectors (1,0,0) and
24       (2,0,0) each also in the y- and z-direction, (1,1,0) and (1,-1,0)  each
25       also  in  the  2  other  planes (these vectors are not independent) and
26       (1,1,1) and the 3 other box diagonals (also not independent). For  each
27       k-vector the sine and cosine are used, in combination with the velocity
28       in 2 perpendicular directions. This gives a total of  16*2*2=64  trans‐
29       verse  currents.  One  autocorrelation  is  calculated  fitted for each
30       k-vector, which gives 16 tcaf's. Each of these tcaf's is fitted to f(t)
31       =  exp(-v)(cosh(Wv) + 1/W sinh(Wv)), v = -t/(2 tau), W = sqrt(1 - 4 tau
32       eta/rho k2), which gives 16 tau's and eta's. The fit weights decay with
33       time  as  exp(-t/wt),  the tcaf and fit are calculated up to time 5*wt.
34       The eta's should be fitted to 1 - a eta(k) k2, from which one can esti‐
35       mate the shear viscosity at k=0.
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38       When  the box is cubic, one can use the option  -oc, which averages the
39       tcaf's over all k-vectors with the same length.  This results  in  more
40       accurate  tcaf's.   Both  the cubic tcaf's and fits are written to  -oc
41       The cubic eta estimates are also written to  -ov.
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44       With option  -mol the transverse current  is  determined  of  molecules
45       instead  of atoms. In this case the index group should consist of mole‐
46       cule numbers instead of atom numbers.
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49       The k-dependent viscosities in the  -ov file should be fitted to eta(k)
50       = eta0 (1 - a k2) to obtain the viscosity at infinite wavelength.
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53       NOTE: make sure you write coordinates and velocities often enough.  The
54       initial, non-exponential, part of the autocorrelation function is  very
55       important for obtaining a good fit.
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FILES

58       -f traj.trr Input
59        Full precision trajectory: trr trj cpt
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61       -s topol.tpr Input, Opt.
62        Structure+mass(db): tpr tpb tpa gro g96 pdb
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64       -n index.ndx Input, Opt.
65        Index file
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67       -ot transcur.xvg Output, Opt.
68        xvgr/xmgr file
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70       -oa tcaf_all.xvg Output
71        xvgr/xmgr file
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73       -o tcaf.xvg Output
74        xvgr/xmgr file
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76       -of tcaf_fit.xvg Output
77        xvgr/xmgr file
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79       -oc tcaf_cub.xvg Output, Opt.
80        xvgr/xmgr file
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82       -ov visc_k.xvg Output
83        xvgr/xmgr file
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85

OTHER OPTIONS

87       -[no]hno
88        Print help info and quit
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90       -[no]versionno
91        Print version info and quit
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93       -nice int 19
94        Set the nicelevel
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96       -b time 0
97        First frame (ps) to read from trajectory
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99       -e time 0
100        Last frame (ps) to read from trajectory
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102       -dt time 0
103        Only use frame when t MOD dt = first time (ps)
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105       -[no]wno
106        View output xvg, xpm, eps and pdb files
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108       -xvg enum xmgrace
109        xvg plot formatting:  xmgrace,  xmgr or  none
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111       -[no]molno
112        Calculate tcaf of molecules
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114       -[no]k34no
115        Also use k=(3,0,0) and k=(4,0,0)
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117       -wt real 5
118        Exponential decay time for the TCAF fit weights
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120       -acflen int -1
121        Length of the ACF, default is half the number of frames
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123       -[no]normalizeyes
124        Normalize ACF
125
126       -P enum 0
127        Order of Legendre polynomial for ACF (0 indicates none):  0,  1,  2 or
128       3
129
130       -fitfn enum none
131        Fit function:  none,  exp,  aexp,   exp_exp,   vac,   exp5,   exp7  or
132       exp9
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134       -ncskip int 0
135        Skip N points in the output file of correlation functions
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137       -beginfit real 0
138        Time where to begin the exponential fit of the correlation function
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140       -endfit real -1
141        Time  where to end the exponential fit of the correlation function, -1
142       is until the end
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO