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)