gmx tcaf¶
Synopsis¶
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>]
Description¶
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¶
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)- Index file
Options to specify output files:
-ot[<.xvg>] (transcur.xvg) (Optional)- xvgr/xmgr file
-oa[<.xvg>] (tcaf_all.xvg)- xvgr/xmgr file
-o[<.xvg>] (tcaf.xvg)- xvgr/xmgr file
-of[<.xvg>] (tcaf_fit.xvg)- xvgr/xmgr file
-oc[<.xvg>] (tcaf_cub.xvg) (Optional)- xvgr/xmgr file
-ov[<.xvg>] (visc_k.xvg)- xvgr/xmgr file
Other options:
-b<time> (0)- Time of first frame to read from trajectory (default unit ps)
-e<time> (0)- Time of last frame to read from trajectory (default unit ps)
-dt<time> (0)- Only use frame when t MOD dt = first time (default unit 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)- Normalize ACF
-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