debian man page for g_angle

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

NAME
       g_angle - calculates distributions and correlations for angles and dihedrals

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS
       g_angle	-f  traj.xtc  -n  angle.ndx  -od  angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oh trhisto.xvg -oc dihcorr.xvg -or
       traj.trr -[no]h -[no]version -nice int -b time -e time -dt  time  -[no]w  -xvg  enum  -type  enum  -[no]all  -binwidth  real  -[no]periodic
       -[no]chandler -[no]avercorr -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real

DESCRIPTION
	 g_angle  computes  the angle distribution for a number of angles or dihedrals. This way you can check whether your simulation is correct.
       With option  -ov you can plot the average angle of a group of angles as a function of time. With the  -all option the first  graph  is  the
       average, the rest are the individual angles.

       With the  -of option,  g_angle also calculates the fraction of trans dihedrals (only for dihedrals) as function of time, but this is proba-
       bly only fun for a selected few.

       With option  -oc a dihedral correlation function is calculated.

       It should be noted that the index file should contain atom-triples for angles or atom-quadruplets for dihedrals.  If this is not the  case,
       the program will crash.

       With option  -or a trajectory file is dumped containing cos and sin of selected dihedral angles which subsequently can be used as input for
       a PCA analysis using  g_covar.

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

       -n angle.ndx Input
	Index file

       -od angdist.xvg Output
	xvgr/xmgr file

       -ov angaver.xvg Output, Opt.
	xvgr/xmgr file

       -of dihfrac.xvg Output, Opt.
	xvgr/xmgr file

       -ot dihtrans.xvg Output, Opt.
	xvgr/xmgr file

       -oh trhisto.xvg Output, Opt.
	xvgr/xmgr file

       -oc dihcorr.xvg Output, Opt.
	xvgr/xmgr file

       -or traj.trr Output, Opt.
	Trajectory in portable xdr format

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

       -type enum angle
	Type of angle to analyse:  angle,  dihedral,  improper or  ryckaert-bellemans

       -[no]allno
	Plot all angles separately in the averages file, in the order of appearance in the index file.

       -binwidth real 1
	binwidth (degrees) for calculating the distribution

       -[no]periodicyes
	Print dihedral angles modulo 360 degrees

       -[no]chandlerno
	Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi   -60	or
       phi  60.

       -[no]avercorrno
	Average the correlation functions for the individual angles/dihedrals

       -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
       - Counting transitions only works for dihedrals with multiplicity 3

SEE ALSO
       gromacs(7)

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

								  Mon 4 Apr 2011							g_angle(1)