1GMX-ANGLE(1)                        GROMACS                       GMX-ANGLE(1)
2
3
4

NAME

6       gmx-angle  -  Calculate  distributions  and correlations for angles and
7       dihedrals
8

SYNOPSIS

10          gmx angle [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-od [<.xvg>]]
11                    [-ov [<.xvg>]] [-of [<.xvg>]] [-ot [<.xvg>]] [-oh [<.xvg>]]
12                    [-oc [<.xvg>]] [-or [<.trr>]] [-b <time>] [-e <time>]
13                    [-dt <time>] [-[no]w] [-xvg <enum>] [-type <enum>]
14                    [-[no]all] [-binwidth <real>] [-[no]periodic]
15                    [-[no]chandler] [-[no]avercorr] [-acflen <int>]
16                    [-[no]normalize] [-P <enum>] [-fitfn <enum>]
17                    [-beginfit <real>] [-endfit <real>]
18

DESCRIPTION

20       gmx angle computes the angle distribution for a  number  of  angles  or
21       dihedrals.
22
23       With option -ov, you can plot the average angle of a group of angles as
24       a function of time. With the -all option, the first graph is the  aver‐
25       age and the rest are the individual angles.
26
27       With  the  -of  option, gmx angle also calculates the fraction of trans
28       dihedrals (only for dihedrals) as function of time, but this is  proba‐
29       bly only fun for a select few.
30
31       With option -oc, a dihedral correlation function is calculated.
32
33       It  should  be noted that the index file must contain atom triplets for
34       angles or atom quadruplets for dihedrals.  If this is not the case, the
35       program will crash.
36
37       With  option -or, a trajectory file is dumped containing cos and sin of
38       selected dihedral angles, which subsequently can be used as input for a
39       principal components analysis using gmx covar.
40
41       Option  -ot  plots  when transitions occur between dihedral rotamers of
42       multiplicity 3 and -oh records a histogram of the  times  between  such
43       transitions, assuming the input trajectory frames are equally spaced in
44       time.
45

OPTIONS

47       Options to specify input files:
48
49       -f [<.xtc/.trr/…>] (traj.xtc)
50              Trajectory: xtc trr cpt gro g96 pdb tng
51
52       -n [<.ndx>] (angle.ndx)
53              Index file
54
55       Options to specify output files:
56
57       -od [<.xvg>] (angdist.xvg)
58              xvgr/xmgr file
59
60       -ov [<.xvg>] (angaver.xvg) (Optional)
61              xvgr/xmgr file
62
63       -of [<.xvg>] (dihfrac.xvg) (Optional)
64              xvgr/xmgr file
65
66       -ot [<.xvg>] (dihtrans.xvg) (Optional)
67              xvgr/xmgr file
68
69       -oh [<.xvg>] (trhisto.xvg) (Optional)
70              xvgr/xmgr file
71
72       -oc [<.xvg>] (dihcorr.xvg) (Optional)
73              xvgr/xmgr file
74
75       -or [<.trr>] (traj.trr) (Optional)
76              Trajectory in portable xdr format
77
78       Other options:
79
80       -b <time> (0)
81              Time of first frame to read from trajectory (default unit ps)
82
83       -e <time> (0)
84              Time of last frame to read from trajectory (default unit ps)
85
86       -dt <time> (0)
87              Only use frame when t MOD dt = first time (default unit ps)
88
89       -[no]w (no)
90              View output .xvg, .xpm, .eps and .pdb files
91
92       -xvg <enum> (xmgrace)
93              xvg plot formatting: xmgrace, xmgr, none
94
95       -type <enum> (angle)
96              Type of angle  to  analyse:  angle,  dihedral,  improper,  ryck‐
97              aert-bellemans
98
99       -[no]all (no)
100              Plot all angles separately in the averages file, in the order of
101              appearance in the index file.
102
103       -binwidth <real> (1)
104              binwidth (degrees) for calculating the distribution
105
106       -[no]periodic (yes)
107              Print dihedral angles modulo 360 degrees
108
109       -[no]chandler (no)
110              Use Chandler correlation function (N[trans] = 1, N[gauche] =  0)
111              rather than cosine correlation function. Trans is defined as phi
112              < -60 or phi > 60.
113
114       -[no]avercorr (no)
115              Average   the   correlation   functions   for   the   individual
116              angles/dihedrals
117
118       -acflen <int> (-1)
119              Length of the ACF, default is half the number of frames
120
121       -[no]normalize (yes)
122              Normalize ACF
123
124       -P <enum> (0)
125              Order  of  Legendre polynomial for ACF (0 indicates none): 0, 1,
126              2, 3
127
128       -fitfn <enum> (none)
129              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
130
131       -beginfit <real> (0)
132              Time where to begin the exponential fit of the correlation func‐
133              tion
134
135       -endfit <real> (-1)
136              Time  where  to end the exponential fit of the correlation func‐
137              tion, -1 is until the end
138

KNOWN ISSUES

140       · Counting transitions only works for dihedrals with multiplicity 3
141

SEE ALSO

143       gmx(1)
144
145       More    information    about    GROMACS    is    available    at     <‐
146       http://www.gromacs.org/>.
147

149       2020, GROMACS development team
150
151
152
153
1542019.6                           Feb 28, 2020                     GMX-ANGLE(1)
Impressum