g_gyrate_d1
Calculate the radius of gyration
Part of gmx-gyrate(1).
Usage
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>]
Overview
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.
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
History
- Debian 8 (Jessie): the text shown here
- Debian 7 (Wheezy)
- Debian 6.0 (Squeeze)
- Debian 5.0 (Lenny)