GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages
GMX-TCAF(1) GROMACS GMX-TCAF(1)

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)
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

gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

2022, GROMACS development team
January 14, 2022 2021.5

Search for    or go to Top of page |  Section 1 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.