g_angle(1)

NAME
g_angle - calculates distributions and correlations for angles and dihedrals VERSION 4.6.2

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. 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 and 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 probably only fun for a select few. With option -oc, a dihedral correlation function is calculated. It should be noted that the index file must contain atom triplets 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 principal components analysis using g_covar. Option -ot plots when transitions occur between dihedral rotamers of multiplicity 3 and -oh records a histogram of the times between such transitions, assuming the input trajectory frames are equally spaced in time.

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 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

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/>.