1GMX-TCAF(1)                         GROMACS                        GMX-TCAF(1)
2
3
4

NAME

6       gmx-tcaf - Calculate viscosities of liquids
7

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>]
15

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.
20
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.
35
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.
40
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.
44
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.
47
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.
51

OPTIONS

53       Options to specify input files:
54
55       -f [<.trr/.cpt/…>] (traj.trr)
56              Full precision trajectory: trr cpt tng
57
58       -s [<.tpr/.gro/…>] (topol.tpr) (Optional)
59              Structure+mass(db): tpr gro g96 pdb brk ent
60
61       -n [<.ndx>] (index.ndx) (Optional)
62              Index file
63
64       Options to specify output files:
65
66       -ot [<.xvg>] (transcur.xvg) (Optional)
67              xvgr/xmgr file
68
69       -oa [<.xvg>] (tcaf_all.xvg)
70              xvgr/xmgr file
71
72       -o [<.xvg>] (tcaf.xvg)
73              xvgr/xmgr file
74
75       -of [<.xvg>] (tcaf_fit.xvg)
76              xvgr/xmgr file
77
78       -oc [<.xvg>] (tcaf_cub.xvg) (Optional)
79              xvgr/xmgr file
80
81       -ov [<.xvg>] (visc_k.xvg)
82              xvgr/xmgr file
83
84       Other options:
85
86       -b <time> (0)
87              Time of first frame to read from trajectory (default unit ps)
88
89       -e <time> (0)
90              Time of last frame to read from trajectory (default unit ps)
91
92       -dt <time> (0)
93              Only use frame when t MOD dt = first time (default unit ps)
94
95       -[no]w (no)
96              View output .xvg, .xpm, .eps and .pdb files
97
98       -xvg <enum> (xmgrace)
99              xvg plot formatting: xmgrace, xmgr, none
100
101       -[no]mol (no)
102              Calculate TCAF of molecules
103
104       -[no]k34 (no)
105              Also use k=(3,0,0) and k=(4,0,0)
106
107       -wt <real> (5)
108              Exponential decay time for the TCAF fit weights
109
110       -acflen <int> (-1)
111              Length of the ACF, default is half the number of frames
112
113       -[no]normalize (yes)
114              Normalize ACF
115
116       -P <enum> (0)
117              Order of Legendre polynomial for ACF (0 indicates none):  0,  1,
118              2, 3
119
120       -fitfn <enum> (none)
121              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
122
123       -beginfit <real> (0)
124              Time where to begin the exponential fit of the correlation func‐
125              tion
126
127       -endfit <real> (-1)
128              Time where to end the exponential fit of the  correlation  func‐
129              tion, -1 is until the end
130

SEE ALSO

132       gmx(1)
133
134       More     information    about    GROMACS    is    available    at    <‐
135       http://www.gromacs.org/>.
136

138       2019, GROMACS development team
139
140
141
142
1432018.7                           May 29, 2019                      GMX-TCAF(1)
Impressum