gmx-angle(1) GROMACS Manual gmx-angle(1)NAMEgmx-angle - Calculate distributions and correlations for angles and
dihedrals
SYNOPSIS
gmx angle [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-od [<.xvg>]]
[-ov [<.xvg>]] [-of [<.xvg>]] [-ot [<.xvg>]] [-oh [<.xvg>]]
[-oc [<.xvg>]] [-or [<.trr>]] [-nice <int>] [-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>]
DESCRIPTION
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 aver‐
age 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 proba‐
bly 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
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-n [<.ndx>] (angle.ndx) (Input)
Index file
-od [<.xvg>] (angdist.xvg) (Output)
xvgr/xmgr file
-ov [<.xvg>] (angaver.xvg) (Output, Optional)
xvgr/xmgr file
-of [<.xvg>] (dihfrac.xvg) (Output, Optional)
xvgr/xmgr file
-ot [<.xvg>] (dihtrans.xvg) (Output, Optional)
xvgr/xmgr file
-oh [<.xvg>] (trhisto.xvg) (Output, Optional)
xvgr/xmgr file
-oc [<.xvg>] (dihcorr.xvg) (Output, Optional)
xvgr/xmgr file
-or [<.trr>] (traj.trr) (Output, Optional)
Trajectory in portable xdr format
Other options:
-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
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-type <enum> (angle)
Type of angle to analyse: angle, dihedral, improper, ryck‐
aert-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/dihe‐
drals
-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, vac, exp5, exp7, exp9, erf‐
fit
-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 ISSUES
- Counting transitions only works for dihedrals with multiplicity 3
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-angle(1)
