1GMX-PRINCIPAL(1) GROMACS GMX-PRINCIPAL(1)
2
3
4
6 gmx-principal - Calculate principal axes of inertia for a group of
7 atoms
8
10 gmx principal [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
11 [-n [<.ndx>]] [-a1 [<.xvg>]] [-a2 [<.xvg>]]
12 [-a3 [<.xvg>]] [-om [<.xvg>]] [-b <time>] [-e <time>]
13 [-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
14 [-[no]foo]
15
17 gmx principal calculates the three principal axes of inertia for a
18 group of atoms. NOTE: Old versions of GROMACS wrote the output data in
19 a strange transposed way. As of GROMACS 5.0, the output file paxis1.dat
20 contains the x/y/z components of the first (major) principal axis for
21 each frame, and similarly for the middle and minor axes in paxis2.dat
22 and paxis3.dat.
23
25 Options to specify input files:
26
27 -f [<.xtc/.trr/…>] (traj.xtc)
28 Trajectory: xtc trr cpt gro g96 pdb tng
29
30 -s [<.tpr/.gro/…>] (topol.tpr)
31 Structure+mass(db): tpr gro g96 pdb brk ent
32
33 -n [<.ndx>] (index.ndx) (Optional)
34 Index file
35
36 Options to specify output files:
37
38 -a1 [<.xvg>] (paxis1.xvg)
39 xvgr/xmgr file
40
41 -a2 [<.xvg>] (paxis2.xvg)
42 xvgr/xmgr file
43
44 -a3 [<.xvg>] (paxis3.xvg)
45 xvgr/xmgr file
46
47 -om [<.xvg>] (moi.xvg)
48 xvgr/xmgr file
49
50 Other options:
51
52 -b <time> (0)
53 Time of first frame to read from trajectory (default unit ps)
54
55 -e <time> (0)
56 Time of last frame to read from trajectory (default unit ps)
57
58 -dt <time> (0)
59 Only use frame when t MOD dt = first time (default unit ps)
60
61 -tu <enum> (ps)
62 Unit for time values: fs, ps, ns, us, ms, s
63
64 -[no]w (no)
65 View output .xvg, .xpm, .eps and .pdb files
66
67 -xvg <enum> (xmgrace)
68 xvg plot formatting: xmgrace, xmgr, none
69
70 -[no]foo (no)
71 Dummy option to avoid empty array
72
74 gmx(1)
75
76 More information about GROMACS is available at <‐
77 http://www.gromacs.org/>.
78
80 2020, GROMACS development team
81
82
83
84
852019.6 Feb 28, 2020 GMX-PRINCIPAL(1)