1g_angle(1) GROMACS suite, VERSION 4.5 g_angle(1)
2
6 g_angle - calculates distributions and correlations for angles and
7 dihedrals
8 VERSION 4.5
10
12 g_angle -f traj.xtc -n angle.ndx -od angdist.xvg -ov angaver.xvg -of
13 dihfrac.xvg -ot dihtrans.xvg -oh trhisto.xvg -oc dihcorr.xvg -or
14 traj.trr -[no]h -[no]version -nice int -b time -e time -dt time -[no]w
15 -xvg enum -type enum -[no]all -binwidth real -[no]periodic -[no]chan‐
16 dler -[no]avercorr -acflen int -[no]normalize -P enum -fitfn enum
17 -ncskip int -beginfit real -endfit real
18
20 g_angle computes the angle distribution for a number of angles or dihe‐
21 drals. This way you can check whether your simulation is correct. With
22 option -ov you can plot the average angle of a group of angles as a
23 function of time. With the -all option the first graph is the average,
24 the rest are the individual angles.
25 With the -of option g_angle also calculates the fraction of trans dihe‐
28 drals (only for dihedrals) as function of time, but this is probably
29 only fun for a selected few.
30 With option -oc a dihedral correlation function is calculated.
33 It should be noted that the indexfile should contain atom-triples for
36 angles or atom-quadruplets for dihedrals. If this is not the case, the
37 program will crash.
38 With option -or a trajectory file is dumped containing cos and sin of
41 selected dihedral angles which subsequently can be used as input for a
42 PCA analysis using g_covar.
43
45 -f traj.xtc Input
46 Trajectory: xtc trr trj gro g96 pdb cpt
47 -n angle.ndx Input
49 Index file
50 -od angdist.xvg Output
52 xvgr/xmgr file
53 -ov angaver.xvg Output, Opt.
55 xvgr/xmgr file
56 -of dihfrac.xvg Output, Opt.
58 xvgr/xmgr file
59 -ot dihtrans.xvg Output, Opt.
61 xvgr/xmgr file
62 -oh trhisto.xvg Output, Opt.
64 xvgr/xmgr file
65 -oc dihcorr.xvg Output, Opt.
67 xvgr/xmgr file
68 -or traj.trr Output, Opt.
70 Trajectory in portable xdr format
71
74 -[no]hno
75 Print help info and quit
76 -[no]versionno
78 Print version info and quit
79 -nice int 19
81 Set the nicelevel
82 -b time 0
84 First frame (ps) to read from trajectory
85 -e time 0
87 Last frame (ps) to read from trajectory
88 -dt time 0
90 Only use frame when t MOD dt = first time (ps)
91 -[no]wno
93 View output xvg, xpm, eps and pdb files
94 -xvg enum xmgrace
96 xvg plot formatting: xmgrace, xmgr or none
97 -type enum angle
99 Type of angle to analyse: angle, dihedral, improper or ryck‐
100 aert-bellemans
101 -[no]allno
103 Plot all angles separately in the averages file, in the order of
104 appearance in the index file.
105 -binwidth real 1
107 binwidth (degrees) for calculating the distribution
108 -[no]periodicyes
110 Print dihedral angles modulo 360 degrees
111 -[no]chandlerno
113 Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather
114 than cosine correlation function. Trans is defined as phi -60 || phi
115 60.
116 -[no]avercorrno
118 Average the correlation functions for the individual angles/dihedrals
119 -acflen int -1
121 Length of the ACF, default is half the number of frames
122 -[no]normalizeyes
124 Normalize ACF
125 -P enum 0
127 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or
128 3
129 -fitfn enum none
131 Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7 or
132 exp9
133 -ncskip int 0
135 Skip N points in the output file of correlation functions
136 -beginfit real 0
138 Time where to begin the exponential fit of the correlation function
139 -endfit real -1
141 Time where to end the exponential fit of the correlation function, -1
142 is until the end
143
146 - Counting transitions only works for dihedrals with multiplicity 3
147
150 gromacs(7)
151 More information about GROMACS is available at <http://www.gro‐
153 macs.org/>.
154 Thu 26 Aug 2010 g_angle(1)