g_rotacf(1) [debian man page]

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

NAME

       g_rotacf - calculates the rotational correlation function for molecules

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_rotacf -f traj.xtc -s topol.tpr -n index.ndx -o rotacf.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]d
       -[no]aver -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real

DESCRIPTION

	g_rotacf calculates the rotational correlation function for molecules. Three atoms (i,j,k) must be given in the index file,  defining  two
       vectors	ij  and  jk. The rotational ACF is calculated as the autocorrelation function of the vector n = ij x jk, i.e. the cross product of
       the two vectors.  Since three atoms span a plane, the order of the three atoms does not matter. Optionally, controlled by the   -d  switch,
       you can calculate the rotational correlation function for linear molecules by specifying two atoms (i,j) in the index file.

       EXAMPLES

	g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1 -beginfit 2.5 -endfit 20.0

       This  will  calculate  the  rotational correlation function using a first order Legendre polynomial of the angle of a vector defined by the
       index file. The correlation function will be fitted from 2.5 ps until 20.0 ps to a two-parameter exponential.

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

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

       -n index.ndx Input
	Index file

       -o rotacf.xvg Output
	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

       -[no]dno
	Use index doublets (vectors) for correlation function instead of triplets (planes)

       -[no]averyes
	Average over molecules

       -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_rotacf(1)

Check Out this Related Man Page

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

NAME

       g_sgangle - computes the angle and distance between two groups

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_sgangle  -f  traj.xtc	-n index.ndx -s topol.tpr -oa sg_angle.xvg -od sg_dist.xvg -od1 sg_dist1.xvg -od2 sg_dist2.xvg -[no]h -[no]version
       -nice int -b time -e time -dt time -[no]w -xvg enum -[no]one -[no]z

DESCRIPTION

       Compute the angle and distance between two groups.  The groups are defined by a number of atoms given in an index file and may  be  two	or
       three  atoms in size.  If  -one is set, only one group should be specified in the index file and the angle between this group at time 0 and
       t will be computed.  The angles calculated depend on the order in which the atoms are given. Giving, for instance, 5 6 will rotate the vec-
       tor 5-6 with 180 degrees compared to giving 6 5.

       If three atoms are given, the normal on the plane spanned by those three atoms will be calculated, using the formula  P1P2 x P1P3.  The cos
       of the angle is calculated, using the inproduct of the two normalized vectors.

       Here is what some of the file options do:

	-oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane	defined  by  those
       three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used.

	-od: Distance between two groups. Distance is taken from the center of one group to the center of the other group.

	-od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately.

	-od2: For two planes this option has no meaning.

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input
	Index file

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

       -oa sg_angle.xvg Output
	xvgr/xmgr file

       -od sg_dist.xvg Output, Opt.
	xvgr/xmgr file

       -od1 sg_dist1.xvg Output, Opt.
	xvgr/xmgr file

       -od2 sg_dist2.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

       -[no]oneno
	Only one group compute angle between vector at time zero and time t

       -[no]zno
	Use the  z-axis as reference

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						      g_sgangle(1)

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g_rotacf(1) [debian man page]

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