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g_gyrate_d
Langue: en
Version: 250691 (debian - 07/07/09)
Section: 1 (Commandes utilisateur)
NAME
g_gyrate - calculates the radius of gyrationSYNOPSIS
g_gyrate -f traj.xtc -s topol.tpr -n index.ndx -o gyrate.xvg -acf moi-acf.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 realDESCRIPTION
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 InputGeneric 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 noPrint 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
gromacs(7)More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.
Contenus ©2006-2024 Benjamin Poulain
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