g_angle(1)
NAME
g_angle - calculates distributions and correlations for angles and
dihedrals
SYNOPSIS
g_angle -f traj.xtc -s topol.tpr -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]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
- Generic trajectory: xtc trr trj gro g96 pdb
- -s topol.tpr Input
- Generic run input: tpr tpb tpa xml
- -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]h no
- 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]w no
- View output xvg, xpm, eps and pdb files
- -[no]xvgr yes
- 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]all no
- 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]chandler no
- Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather
- than cosine correlation function. Trans is defined as phi -60 || phi 60.
- -[no]avercorr no
- Average the correlation functions for the individual angles/dihedrals
- -acflen int -1
- Length of the ACF, default is half the number of frames
- -[no]normalize yes
- 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
- - Counting transitions only works for dihedrals with multiplicity 3
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.