g_gyrate

Main Table of Contents

VERSION 4.6.7
Fri 29 Aug 2014


Description

g_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.

Files

optionfilenametypedescription
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb
-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

optiontypedefaultdescription
-[no]h bool no Print help info and quit
-[no]version bool no Print version 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 bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-nmol int 1 The number of molecules to analyze
-[no]q bool no Use absolute value of the charge of an atom as weighting factor instead of mass
-[no]p bool no Calculate the radii of gyration about the principal axes.
-[no]moi bool 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 bool 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, exp9 or erffit
-ncskip int 0 Skip this many 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 until the end


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