1GMX-ANGLE(1)                        GROMACS                       GMX-ANGLE(1)
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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.
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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.
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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.
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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.
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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.
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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.
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OPTIONS

47       Options to specify input files:
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49       -f [<.xtc/.trr/…>] (traj.xtc)
50              Trajectory: xtc trr cpt gro g96 pdb tng
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52       -n [<.ndx>] (angle.ndx)
53              Index file
54
55       Options to specify output files:
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57       -od [<.xvg>] (angdist.xvg)
58              xvgr/xmgr file
59
60       -ov [<.xvg>] (angaver.xvg) (Optional)
61              xvgr/xmgr file
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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
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72       -oc [<.xvg>] (dihcorr.xvg) (Optional)
73              xvgr/xmgr file
74
75       -or [<.trr>] (traj.trr) (Optional)
76              Trajectory in portable xdr format
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78       Other options:
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80       -b <time> (0)
81              Time of first frame to read from trajectory (default unit ps)
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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
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95       -type <enum> (angle)
96              Type of angle  to  analyse:  angle,  dihedral,  improper,  ryck‐
97              aert-bellemans
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99       -[no]all (no)
100              Plot all angles separately in the averages file, in the order of
101              appearance in the index file.
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103       -binwidth <real> (1)
104              binwidth (degrees) for calculating the distribution
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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
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SEE ALSO

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

149       2019, GROMACS development team
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1542019.4                           Oct 02, 2019                     GMX-ANGLE(1)
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