gmx-angle man page
gmx-angle — Calculate distributions and correlations for angles and dihedrals gmx angle computes the angle distribution for a number of angles or dihedrals. Options to specify input files: Options to specify output files: Other options: gmx(1) 2016, GROMACS development team gmx(1).
gmx angle [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-od [<.xvg>]]
[-ov [<.xvg>]] [-of [<.xvg>]] [-ot [<.xvg>]] [-oh [<.xvg>]]
[-oc [<.xvg>]] [-or [<.trr>]] [-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>]
[-beginfit <real>] [-endfit <real>]
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, gmx 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 gmx 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.
More information about GROMACS is available at <http://www.gromacs.org/>.
gmx angle computes the angle distribution for a number of angles or dihedrals.
Options to specify input files:
Options to specify output files:
2016, GROMACS development team