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g_gyrate(1) [debian man page]

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

NAME
g_gyrate - calculates the radius of gyration VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_gyrate -f traj.xtc -s topol.tpr -n index.ndx -o gyrate.xvg -acf moi-acf.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -nmol int -[no]q -[no]p -[no]moi -nz int -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION
g_gyrate computes the radius of gyration of a group of atoms and the radii of gyration about the x-, y- and z-axes, as a function of time. The atoms are explicitly mass weighted. With the -nmol option the radius of gyration will be calculated for multiple molecules by splitting the analysis group in equally sized parts. With the option -nz 2D radii of gyration in the x-y plane of slices along the z-axis are calculated. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -o gyrate.xvg Output xvgr/xmgr file -acf moi-acf.xvg Output, Opt. 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 -nmol int 1 The number of molecules to analyze -[no]qno Use absolute value of the charge of an atom as weighting factor instead of mass -[no]pno Calculate the radii of gyration about the principal axes. -[no]moino Calculate the moments of inertia (defined by the principal axes). -nz int 0 Calculate the 2D radii of gyration of slices along the z-axis -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_gyrate(1)

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

NAME
g_velacc - calculates velocity autocorrelation functions VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_velacc -f traj.trr -s topol.tpr -n index.ndx -o vac.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]m -[no]mol -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION
g_velacc computes the velocity autocorrelation function. When the -m option is used, the momentum autocorrelation function is calcu- lated. With option -mol the velocity autocorrelation function of molecules is calculated. In this case the index group should consist of molecule numbers instead of atom numbers. 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 -o vac.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]mno Calculate the momentum autocorrelation function -[no]molno Calculate the velocity acf of 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_velacc(1)
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