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gmx-gyrate(1)                   GROMACS Manual                   gmx-gyrate(1)

NAME
       gmx-gyrate - Calculate the radius of gyration

SYNOPSIS
       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.

       The axis components corresponds to the mass-weighted root-mean-square
       of the radii components orthogonal to each axis, for example:

       Rg(x) = sqrt((sum_i m_i (R_i(y)2 + R_i(z)2))/(sum_i m_i)).

       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 5.0.6                                                    gmx-gyrate(1)