g_gyrate(1) [debian man page]

g_gyrate(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       g_gyrate(1)

NAME

       g_gyrate - calculates the radius of gyration

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_gyrate -f traj.xtc -s topol.tpr -n index.ndx -o gyrate.xvg -acf moi-acf.xvg -[no]h -[no]version -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 -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.

       With the option	-nz 2D radii of gyration in the  x-y plane of slices along the	z-axis are calculated.

FILES

       -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

       -[no]hno
	Print help info and quit

       -[no]versionno
	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]wno
	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]qno
	Use absolute value of the charge of an atom as weighting factor instead of mass

       -[no]pno
	Calculate the radii of gyration about the principal axes.

       -[no]moino
	Calculate the moments of inertia (defined by the principal axes).

       -nz int 0
	Calculate the 2D radii of gyration of  slices along the z-axis

       -acflen int -1
	Length of the ACF, default is half the number of frames

       -[no]normalizeyes
	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 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 until the end

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						       g_gyrate(1)

g_dos(1)						   GROMACS suite, VERSION 4.5.5 						  g_dos(1)

NAME

       g_dos - compute density of states from a simulation trajectory VERSION 4.5.5

SYNOPSIS

       g_dos  -f  traj.trr -s topol.tpr -n index.ndx -vacf vacf.xvg -mvacf mvacf.xvg -dos dos.xvg -g dos.log -[no]h -[no]version -nice int -b time
       -e time -dt time -[no]w -xvg enum -[no]v -[no]recip -[no]abs -[no]normdos -T real -acflen int -[no]normalize -P enum  -fitfn  enum  -ncskip
       int -beginfit real -endfit real

DESCRIPTION

	g_dos computes the Density of States from a simulation.  In order for this to be meaningful the velocities must be saved in the trajectory
       with sufficiently high frequency such as to cover all vibrations. For flexible systems that would be around a few fs between saving.  Prop-
       erties based on the DoS are printed on the standard output.

FILES

       -f traj.trr Input
	Full precision trajectory: trr trj cpt

       -s topol.tpr Input
	Run input file: tpr tpb tpa

       -n index.ndx Input, Opt.
	Index file

       -vacf vacf.xvg Output
	xvgr/xmgr file

       -mvacf mvacf.xvg Output
	xvgr/xmgr file

       -dos dos.xvg Output
	xvgr/xmgr file

       -g dos.log Output
	Log file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	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]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -[no]vyes
	Be loud and noisy.

       -[no]recipno
	Use cm-1 on X-axis instead of 1/ps for DoS plots.

       -[no]absno
	Use the absolute value of the Fourier transform of the VACF as the Density of States. Default is to use the real component only

       -[no]normdosno
	Normalize the DoS such that it adds up to 3N. This is a hack that should not be necessary.

       -T real 298.15
	Temperature in the simulation

       -acflen int -1
	Length of the ACF, default is half the number of frames

       -[no]normalizeyes
	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 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 until the end

KNOWN PROBLEMS

       -  This program needs a lot of memory: total usage equals the number of atoms times 3 times number of frames times 4 (or 8 when run in dou-
       ble precision).

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Wed 21 Sep 2011							  g_dos(1)