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g_rotacf(1) [debian man page]

g_rotacf(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       g_rotacf(1)

NAME
g_rotacf - calculates the rotational correlation function for molecules VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_rotacf -f traj.xtc -s topol.tpr -n index.ndx -o rotacf.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]d -[no]aver -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION
g_rotacf calculates the rotational correlation function for molecules. Three atoms (i,j,k) must be given in the index file, defining two vectors ij and jk. The rotational ACF is calculated as the autocorrelation function of the vector n = ij x jk, i.e. the cross product of the two vectors. Since three atoms span a plane, the order of the three atoms does not matter. Optionally, controlled by the -d switch, you can calculate the rotational correlation function for linear molecules by specifying two atoms (i,j) in the index file. EXAMPLES g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1 -beginfit 2.5 -endfit 20.0 This will calculate the rotational correlation function using a first order Legendre polynomial of the angle of a vector defined by the index file. The correlation function will be fitted from 2.5 ps until 20.0 ps to a two-parameter exponential. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input Run input file: tpr tpb tpa -n index.ndx Input Index file -o rotacf.xvg Output xvgr/xmgr file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -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]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]dno Use index doublets (vectors) for correlation function instead of triplets (planes) -[no]averyes Average over molecules -acflen int -1 Length of the ACF, default is half the number of frames -[no]normalizeyes Normalize ACF -P enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 -fitfn enum none Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit -ncskip int 0 Skip N points in the output file of correlation functions -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 SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_rotacf(1)

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g_tcaf(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					 g_tcaf(1)

NAME
g_tcaf - calculates viscosities of liquids VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_tcaf -f traj.trr -s topol.tpr -n index.ndx -ot transcur.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg -oc tcaf_cub.xvg -ov visc_k.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]mol -[no]k34 -wt real -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION
g_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 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 values of tau and eta. The fit weights decay with time as exp(-t/wt), and the TCAF and fit are calculated up to time 5*wt. The eta values 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 -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 mol- ecule numbers instead of atom numbers. The k-dependent viscosities in the -ov file 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. FILES
-f traj.trr Input Full precision trajectory: trr trj cpt -s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -ot transcur.xvg Output, Opt. xvgr/xmgr file -oa tcaf_all.xvg Output xvgr/xmgr file -o tcaf.xvg Output xvgr/xmgr file -of tcaf_fit.xvg Output xvgr/xmgr file -oc tcaf_cub.xvg Output, Opt. xvgr/xmgr file -ov visc_k.xvg Output xvgr/xmgr file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -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]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]molno Calculate tcaf of molecules -[no]k34no 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]normalizeyes Normalize ACF -P enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 -fitfn enum none Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit -ncskip int 0 Skip N points in the output file of correlation functions -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 SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_tcaf(1)

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