1 .TH g_gyrate 1 "Fri 19 Apr 2013" "" "GROMACS suite, VERSION 4.5.7"
3 g_gyrate - calculates the radius of gyration
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-o" " gyrate.xvg "
12 .BI "\-acf" " moi\-acf.xvg "
14 .BI "\-[no]version" ""
26 .BI "\-acflen" " int "
27 .BI "\-[no]normalize" ""
29 .BI "\-fitfn" " enum "
30 .BI "\-ncskip" " int "
31 .BI "\-beginfit" " real "
32 .BI "\-endfit" " real "
34 \&\fB g_gyrate\fR computes the radius of gyration of a group of atoms
35 \&and the radii of gyration about the \fI x\fR\-, \fI y\fR\- and \fI z\fR\-axes,
36 \&as a function of time. The atoms are explicitly mass weighted.
39 \&With the \fB \-nmol\fR option the radius of gyration will be calculated
40 \&for multiple molecules by splitting the analysis group in equally
44 \&With the option \fB \-nz\fR 2D radii of gyration in the \fI x\-y\fR plane
45 \&of slices along the \fI z\fR\-axis are calculated.
49 Trajectory: xtc trr trj gro g96 pdb cpt
51 .BI "\-s" " topol.tpr"
53 Structure+mass(db): tpr tpb tpa gro g96 pdb
55 .BI "\-n" " index.ndx"
59 .BI "\-o" " gyrate.xvg"
63 .BI "\-acf" " moi\-acf.xvg"
69 Print help info and quit
71 .BI "\-[no]version" "no "
72 Print version info and quit
74 .BI "\-nice" " int" " 19"
77 .BI "\-b" " time" " 0 "
78 First frame (ps) to read from trajectory
80 .BI "\-e" " time" " 0 "
81 Last frame (ps) to read from trajectory
83 .BI "\-dt" " time" " 0 "
84 Only use frame when t MOD dt = first time (ps)
87 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
89 .BI "\-xvg" " enum" " xmgrace"
90 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
92 .BI "\-nmol" " int" " 1"
93 The number of molecules to analyze
96 Use absolute value of the charge of an atom as weighting factor instead of mass
99 Calculate the radii of gyration about the principal axes.
101 .BI "\-[no]moi" "no "
102 Calculate the moments of inertia (defined by the principal axes).
104 .BI "\-nz" " int" " 0"
105 Calculate the 2D radii of gyration of this number of slices along the z\-axis
107 .BI "\-acflen" " int" " \-1"
108 Length of the ACF, default is half the number of frames
110 .BI "\-[no]normalize" "yes "
113 .BI "\-P" " enum" " 0"
114 Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR
116 .BI "\-fitfn" " enum" " none"
117 Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
119 .BI "\-ncskip" " int" " 0"
120 Skip this many points in the output file of correlation functions
122 .BI "\-beginfit" " real" " 0 "
123 Time where to begin the exponential fit of the correlation function
125 .BI "\-endfit" " real" " \-1 "
126 Time where to end the exponential fit of the correlation function, \-1 is until the end
131 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.