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GMX-GYRATE-LEGACY(1)		    GROMACS		  GMX-GYRATE-LEGACY(1)

NAME
       gmx-gyrate-legacy - Calculate the radius	of gyration

SYNOPSIS
	  gmx gyrate-legacy [-f	[<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
		       [-n [<.ndx>]] [-o [<.xvg>]] [-acf [<.xvg>]] [-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-legacy 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	files:

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

       -s [<.tpr/.gro/...>] (topol.tpr)
	      Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
	      Index file

       Options to specify output files:

       -o [<.xvg>] (gyrate.xvg)
	      xvgr/xmgr	file

       -acf [<.xvg>] (moi-acf.xvg) (Optional)
	      xvgr/xmgr	file

       Other options:

       -b <time> (0)
	      Time of first frame to read from trajectory (default unit	ps)

       -e <time> (0)
	      Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
	      Only use frame when t MOD	dt = first time	(default unit 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, exp5, exp7, exp9

       -beginfit <real>	(0)
	      Time where to begin the exponential fit of the correlation func-
	      tion

       -endfit <real> (-1)
	      Time where to end	the exponential	fit of the  correlation	 func-
	      tion, -1 is until	the end

SEE ALSO
       gmx(1)

       More	information    about	GROMACS	   is	 available    at    <-
       http://www.gromacs.org/>.

COPYRIGHT
       2025, GROMACS development team

2025.0				 Feb 10, 2025		  GMX-GYRATE-LEGACY(1)

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