g_gyrate(1)
NAME
g_gyrate - calculates the radius of gyration
SYNOPSIS
g_gyrate -f traj.xtc -s topol.tpr -n index.ndx -o gyrate.xvg -acf moiacf.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -nmol int -[no]q -[no]p -[no]moi -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real
DESCRIPTION
g_gyrate computes the radius of gyration of a group of atoms 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.
FILES
- -f traj.xtc Input
- Generic trajectory: xtc trr trj gro g96 pdb
- -s topol.tpr Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
- -n index.ndx Input, Opt.
- Index file
- -o gyrate.xvg Output
- xvgr/xmgr file
- -acf moi-acf.xvg Output, Opt.
- xvgr/xmgr file
OTHER OPTIONS
- -[no]h no
- Print help info and quit
- -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
- -[no]xvgr yes
- Add specific codes (legends etc.) in the output xvg files for the
- xmgrace program
- -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).
- -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 or
- 3
- -fitfn enum none
- Fit function: none , exp , aexp , exp_exp , vac , exp5 , exp7 or exp9
- -ncskip int 0
- Skip N points in the output file of correlation functions
- -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 till the end
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.