gmx gyrate
	Main Table of Contents	VERSION 5.0.6

Synopsis

gmx gyrate [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
           [-o [<.xvg>]] [-acf [<.xvg>]] [-nice ] [-b ]
           [-e ] [-dt ] [-[no]w] [-xvg ] [-nmol ]
           [-[no]q] [-[no]p] [-[no]moi] [-nz ] [-acflen ]
           [-[no]normalize] [-P ] [-fitfn ] [-beginfit ]
           [-endfit ]

Description

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

-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

-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