g_angle

| ## g_angle Main Table of Contents | VERSION 4.5 Thu 26 Aug 2010

### 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 and sin of selected dihedral angles which subsequently can be used as input for a PCA analysis using `g_covar`.

### Files

option | filename | type | description
--- | --- | --- | ---
`-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

option | type | default | description
--- | --- | --- | ---
`-[no]h` | gmx_bool | `no` | Print help info and quit
`-[no]version` | gmx_bool | `no` | 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]w` | gmx_bool | `no` | 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]all` | gmx_bool | `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]periodic` | gmx_bool | `yes` | Print dihedral angles modulo 360 degrees
`-[no]chandler` | gmx_bool | `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` | gmx_bool | `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` | gmx_bool | `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 until the end

### Known problems

- Counting transitions only works for dihedrals with multiplicity 3

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