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gmx-gyrate(1) | GROMACS Manual | gmx-gyrate(1) |
NAME¶
gmx-gyrate - Calculate the radius of gyrationSYNOPSIS¶
gmx gyrate [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]][-n [<.ndx>]] [-o [<.xvg>]] [-acf [<.xvg>]] [-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>] [-beginfit <real>] [-endfit <real>]
DESCRIPTION¶
gmx gyrate computes the radius of gyration of a molecule 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.OPTIONS¶
Options to specify input and output files: -f [<.xtc/.trr/...>] (traj.xtc) (Input)Trajectory: xtc trr cpt trj gro g96 pdb tng -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent -n [<.ndx>] (index.ndx) (Input, Optional)
Index file -o [<.xvg>] (gyrate.xvg) (Output)
xvgr/xmgr file -acf [<.xvg>] (moi-acf.xvg) (Output, Optional)
xvgr/xmgr file Other options: -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]w (no)
View output .xvg, .xpm, .eps and .pdb files -xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none -nmol <int> (1)
The number of molecules to analyze -[no]q (no)
Use absolute value of the charge of an atom as weighting factor instead of mass -[no]p (no)
Calculate the radii of gyration about the principal axes. -[no]moi (no)
Calculate the moments of inertia (defined by the principal axes). -nz <int> (0)
Calculate the 2D radii of gyration of this number of slices along the z-axis -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, vac, exp5, exp7, exp9, erffit -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/>.VERSION 5.0.2 |