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
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