gmx-angle - Calculate distributions and correlations for angles and dihedrals

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>*]

**gmx angle** computes the angle distribution for a number of angles or
dihedrals.

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.

Options to specify input files:

**-f** [<.xtc/.trr/...>] (traj.xtc)
- Trajectory: xtc trr cpt gro g96 pdb tng

**-n** [<.ndx>] (angle.ndx)
- Index file

Options to specify output files:

**-od** [<.xvg>] (angdist.xvg)
- xvgr/xmgr file

**-ov** [<.xvg>] (angaver.xvg)
(Optional)
- xvgr/xmgr file

**-of** [<.xvg>] (dihfrac.xvg)
(Optional)
- xvgr/xmgr file

**-ot** [<.xvg>] (dihtrans.xvg)
(Optional)
- xvgr/xmgr file

**-oh** [<.xvg>] (trhisto.xvg)
(Optional)
- xvgr/xmgr file

**-oc** [<.xvg>] (dihcorr.xvg)
(Optional)
- xvgr/xmgr file

**-or** [<.trr>] (traj.trr) (Optional)
- Trajectory in portable xdr format

Other options:

**-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

**-xvg** <enum> (xmgrace)
- xvg plot formatting: xmgrace, xmgr, none

**-type** <enum> (angle)
- Type of angle to analyse: angle, dihedral, improper,
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]periodic** (yes)
- Print dihedral angles modulo 360 degrees

**-[no]chandler** (no)
- 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]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, 3

**-fitfn** <enum> (none)
- Fit function: none, exp, aexp, exp_exp, exp5, exp7,
exp9

**-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

- •
- Counting transitions only works for dihedrals with
multiplicity 3

**gmx(1)**

More information about GROMACS is available at <

*http://www.gromacs.org/*>.

2017, GROMACS development team