NAME
g_angle - calculates distributions and correlations for angles and
dihedrals
VERSION 4.0.1
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 -nice int -b time -e time -dt time -[no]w -[no]xvgr
-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
probably only fun for a selected few.
With option -oc a dihedral correlation function is calculated.
It should be noted that the indexfile 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 andsin 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
-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
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-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 || 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 or
exp9
-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 till 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/>.
Thu 16 Oct 2008 g_angle(1)