gmx-tcaf man page
gmx-tcaf — Calculate viscosities of liquids
gmx tcaf [-f [<.trr/.cpt/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-ot [<.xvg>]] [-oa [<.xvg>]] [-o [<.xvg>]] [-of [<.xvg>]] [-oc [<.xvg>]] [-ov [<.xvg>]] [-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>]
gmx tcaf 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 y- and z-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 k^2), which gives 16 values of tau and eta. The fit weights decay exponentially with time constant w (given with -wt) 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) k^2, 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 TCAFs over all k-vectors with the same length. This results in more accurate TCAFs. Both the cubic TCAFs 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) = eta_0 (1 - a k^2) 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.
Options to specify input files:
- -f [<.trr/.cpt/...>] (traj.trr)
Full precision trajectory: trr cpt tng
- -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
Structure+mass(db): tpr gro g96 pdb brk ent
- -n [<.ndx>] (index.ndx) (Optional)
Options to specify output files:
- -ot [<.xvg>] (transcur.xvg) (Optional)
- -oa [<.xvg>] (tcaf_all.xvg)
- -o [<.xvg>] (tcaf.xvg)
- -of [<.xvg>] (tcaf_fit.xvg)
- -oc [<.xvg>] (tcaf_cub.xvg) (Optional)
- -ov [<.xvg>] (visc_k.xvg)
- -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)
- -[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
- -xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
- -[no]mol (no)
Calculate TCAF of molecules
- -[no]k34 (no)
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
- -[no]normalize (yes)
- -P <enum> (0)
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
- -fitfn <enum> (none)
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
- -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 until the end
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