gmx gyrate¶
Synopsis¶
gmx gyrate [-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
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