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g_tcaf - calculates viscosities of liquidsVERSION4.0.1

g_tcaf-ftraj.trr-stopol.tpr-nindex.ndx-ottranscur.xvg-oatcaf_all.xvg-otcaf.xvg-oftcaf_fit.xvg-octcaf_cub.xvg-ovvisc_k.xvg-[no]h-niceint-btime-etime-dttime-[no]w-[no]xvgr-[no]mol-[no]k34-wtreal-acflenint-[no]normalize-Penum-fitfnenum-ncskipint-beginfitreal-endfitreal

g_tcaf computes tranverse current autocorrelations. These are used to estimate the shear viscosity eta. For details see: Palmer, JCP 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 plains (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 tcaf’s. Each of these tcaf’s is fitted to f(t) = exp(-v)(cosh(Wv) + 1/W sinh(Wv)), v = -t/(2 tau), W = sqrt(1 - 4 tau eta/rho k2), which gives 16 tau’s and eta’s. The fit weights decay with time as exp(-t/wt), the tcaf and fit are calculated up to time 5*wt. The eta’s should be fitted to 1 - a eta(k) k2, 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 tcaf’s over all k-vectors with the same length. This results in more accurate tcaf’s. Both the cubic tcaf’s and fits are written to-ocThe cubic eta estimates are also written to-ov. With option-molthe 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-ovfile should be fitted to eta(k) = eta0 (1 - a k2) 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.

-ftraj.trrInputFull precision trajectory: trr trj cpt-stopol.tprInput,Opt.Structure+mass(db): tpr tpb tpa gro g96 pdb-nindex.ndxInput,Opt.Index file-ottranscur.xvgOutput,Opt.xvgr/xmgr file-oatcaf_all.xvgOutputxvgr/xmgr file-otcaf.xvgOutputxvgr/xmgr file-oftcaf_fit.xvgOutputxvgr/xmgr file-octcaf_cub.xvgOutput,Opt.xvgr/xmgr file-ovvisc_k.xvgOutputxvgr/xmgr file

-[no]hnoPrint help info and quit-niceint19Set the nicelevel-btime0First frame (ps) to read from trajectory-etime0Last frame (ps) to read from trajectory-dttime0Only use frame when t MOD dt = first time (ps)-[no]wnoView output xvg, xpm, eps and pdb files-[no]xvgryesAdd specific codes (legends etc.) in the output xvg files for the xmgrace program-[no]molnoCalculate tcaf of molecules-[no]k34noAlso use k=(3,0,0) and k=(4,0,0)-wtreal5Exponential decay time for the TCAF fit weights-acflenint-1Length of the ACF, default is half the number of frames-[no]normalizeyesNormalize ACF-Penum0Order of Legendre polynomial for ACF (0 indicates none):0,1,2or3-fitfnenumnoneFit function:none,exp,aexp,exp_exp,vac,exp5,exp7orexp9-ncskipint0Skip N points in the output file of correlation functions-beginfitreal0Time where to begin the exponential fit of the correlation function-endfitreal-1Time where to end the exponential fit of the correlation function, -1 is till the end

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Thu 16 Oct 2008 g_tcaf(1)