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Man Pages


Manual Reference Pages  -  GMX-GYRATE (1)

NAME

gmx-gyrate - Calculate the radius of gyration

CONTENTS

Synopsis
Description
Options
See Also

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/>.

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VERSION 5.0.6 GMX-GYRATE (1)

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