gmx gyrate-legacy#

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