.TH gmx-gyrate 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-gyrate \- Calculate the radius of gyration

.SH 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>]

.SH DESCRIPTION
\fBgmx gyrate\fR computes the radius of gyration of a molecule and the radii of gyration about the \fIx\fR\-, \fIy\fR\- and \fIz\fR\-axes, as a function of time. The atoms are explicitly mass weighted.

With the \fB\-nmol\fR option the radius of gyration will be calculated for multiple molecules by splitting the analysis group in equally sized parts.

With the option \fB\-nz\fR 2D radii of gyration in the \fIx\-y\fR plane of slices along the \fIz\fR\-axis are calculated.

.SH OPTIONS
Options to specify input and output files:

.BI "\-f" " [<.xtc/.trr/...>] (traj.xtc) (Input)"
    Trajectory: xtc trr cpt trj gro g96 pdb tng

.BI "\-s" " [<.tpr/.tpb/...>] (topol.tpr) (Input)"
    Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

.BI "\-n" " [<.ndx>] (index.ndx) (Input, Optional)"
    Index file

.BI "\-o" " [<.xvg>] (gyrate.xvg) (Output)"
    xvgr/xmgr file

.BI "\-acf" " [<.xvg>] (moi-acf.xvg) (Output, Optional)"
    xvgr/xmgr file


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-dt" " <time> (0)"
    Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w" "  (no)"
    View output \fB.xvg\fR, \fB.xpm\fR, \fB.eps\fR and \fB.pdb\fR files

.BI "\-xvg" " <enum> (xmgrace)"
    xvg plot formatting: xmgrace, xmgr, none

.BI "\-nmol" " <int> (1)"
    The number of molecules to analyze

.BI "\-[no]q" "  (no)"
    Use absolute value of the charge of an atom as weighting factor instead of mass

.BI "\-[no]p" "  (no)"
    Calculate the radii of gyration about the principal axes.

.BI "\-[no]moi" "  (no)"
    Calculate the moments of inertia (defined by the principal axes).

.BI "\-nz" " <int> (0)"
    Calculate the 2D radii of gyration of this number of slices along the z\-axis

.BI "\-acflen" " <int> (-1)"
    Length of the ACF, default is half the number of frames

.BI "\-[no]normalize" "  (yes)"
    Normalize ACF

.BI "\-P" " <enum> (0)"
    Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3

.BI "\-fitfn" " <enum> (none)"
    Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9, erffit

.BI "\-beginfit" " <real> (0)"
    Time where to begin the exponential fit of the correlation function

.BI "\-endfit" " <real> (-1)"
    Time where to end the exponential fit of the correlation function, \-1 is until the end


.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.