This is the command gmx-tcaf that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-tcaf - Calculate viscosities of liquids
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)
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>
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
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