Man Linux: Main Page and Category List

g_gyrate - calculates the radius of gyrationVERSION4.0.1

g_gyrate-ftraj.xtc-stopol.tpr-nindex.ndx-ogyrate.xvg-acfmoi-acf.xvg-[no]h-niceint-btime-etime-dttime-[no]w-[no]xvgr-nmolint-[no]q-[no]p-[no]moi-nzint-acflenint-[no]normalize-Penum-fitfnenum-ncskipint-beginfitreal-endfitreal

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-nmoloption the radius of gyration will be calculated for multiple molecules by splitting the analysis group in equally sized parts. With the option-nz2D radii of gyration in the x-y plane of slices along the z-axis are calculated.

-ftraj.xtcInputTrajectory: xtc trr trj gro g96 pdb cpt-stopol.tprInputStructure+mass(db): tpr tpb tpa gro g96 pdb-nindex.ndxInput,Opt.Index file-ogyrate.xvgOutputxvgr/xmgr file-acfmoi-acf.xvgOutput,Opt.xvgr/xmgr file

-[no]hnoPrint help info and quit-niceint19Set the nicelevel-btime0First frame (ps) to read from trajectory-etime0Last frame (ps) to read from trajectory-dttime0Only use frame when t MOD dt = first time (ps)-[no]wnoView output xvg, xpm, eps and pdb files-[no]xvgryesAdd specific codes (legends etc.) in the output xvg files for the xmgrace program-nmolint1The number of molecules to analyze-[no]qnoUse absolute value of the charge of an atom as weighting factor instead of mass-[no]pnoCalculate the radii of gyration about the principal axes.-[no]moinoCalculate the moments of inertia (defined by the principal axes).-nzint0Calculate the 2D radii of gyration of slices along the z-axis-acflenint-1Length of the ACF, default is half the number of frames-[no]normalizeyesNormalize ACF-Penum0Order of Legendre polynomial for ACF (0 indicates none):0,1,2or3-fitfnenumnoneFit function:none,exp,aexp,exp_exp,vac,exp5,exp7orexp9-ncskipint0Skip N points in the output file of correlation functions-beginfitreal0Time where to begin the exponential fit of the correlation function-endfitreal-1Time where to end the exponential fit of the correlation function, -1 is till the end

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Thu 16 Oct 2008 g_gyrate(1)