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
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
-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
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
The cubic eta estimates are also written to
-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
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:
-s[<.tpr/.gro/…>] (topol.tpr) (Optional)
-n[<.ndx>] (index.ndx) (Optional)
Options to specify output files:
-ot[<.xvg>] (transcur.xvg) (Optional)
-oc[<.xvg>] (tcaf_cub.xvg) (Optional)
Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
xvg plot formatting: xmgrace, xmgr, none
Calculate TCAF of molecules
Also use k=(3,0,0) and k=(4,0,0)
Exponential decay time for the TCAF fit weights
Length of the ACF, default is half the number of frames
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
Time where to begin the exponential fit of the correlation function
Time where to end the exponential fit of the correlation function, -1 is until the end