Provided by: gromacs-data_4.6.5-1build1_all 
NAME
g_angle - calculates distributions and correlations for angles and dihedrals
VERSION 4.6.5
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/>.
Mon 2 Dec 2013 g_angle(1)