g_rmsdist(1)

1g_rmGsRdOiMsAtC(S1)suite, VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7gb_ar-mdsidritsyt(1)
2
3
4

NAME

6       g_rmsdist  -  calculates atom pair distances averaged with power -2, -3
7       or -6
8
9       VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty
10

SYNOPSIS

12       g_rmsdist -f traj.xtc -s topol.tpr -n  index.ndx  -equiv  equiv.dat  -o
13       distrmsd.xvg -rms rmsdist.xpm -scl rmsscale.xpm -mean rmsmean.xpm -nmr3
14       nmr3.xpm -nmr6 nmr6.xpm -noe noe.dat -[no]h -[no]version -nice  int  -b
15       time -e time -dt time -[no]w -xvg enum -nlevels int -max real -[no]sumh
16       -[no]pbc
17

DESCRIPTION

19       g_rmsdist computes the root mean square deviation  of  atom  distances,
20       which  has  the  advantage  that  no fit is needed like in standard RMS
21       deviation as computed by g_rms.  The reference structure is taken  from
22       the structure file.  The rmsd at time t is calculated as the rms of the
23       differences in distance between atom-pairs in the  reference  structure
24       and the structure at time t.
25
26
27       g_rmsdist can also produce matrices of the rms distances, rms distances
28       scaled with the mean distance and the mean distances and matrices  with
29       NMR  averaged  distances  (1/r3  and 1/r6 averaging). Finally, lists of
30       atom pairs with 1/r3 and 1/r6 averaged distance below the maximum  dis‐
31       tance ( -max, which will default to 0.6 in this case) can be generated,
32       by default averaging over equivalent hydrogens (all triplets of  hydro‐
33       gens named *[123]). Additionally a list of equivalent atoms can be sup‐
34       plied ( -equiv), each line containing a set of equivalent atoms  speci‐
35       fied as residue number and name and atom name; e.g.:
36
37
38        3 SER  HB1 3 SER  HB2
39
40
41       Residue  and atom names must exactly match those in the structure file,
42       including case. Specifying non-sequential atoms is undefined.
43

FILES

45       -f traj.xtc Input
46        Trajectory: xtc trr trj gro g96 pdb cpt
47
48       -s topol.tpr Input
49        Structure+mass(db): tpr tpb tpa gro g96 pdb
50
51       -n index.ndx Input, Opt.
52        Index file
53
54       -equiv equiv.dat Input, Opt.
55        Generic data file
56
57       -o distrmsd.xvg Output
58        xvgr/xmgr file
59
60       -rms rmsdist.xpm Output, Opt.
61        X PixMap compatible matrix file
62
63       -scl rmsscale.xpm Output, Opt.
64        X PixMap compatible matrix file
65
66       -mean rmsmean.xpm Output, Opt.
67        X PixMap compatible matrix file
68
69       -nmr3 nmr3.xpm Output, Opt.
70        X PixMap compatible matrix file
71
72       -nmr6 nmr6.xpm Output, Opt.
73        X PixMap compatible matrix file
74
75       -noe noe.dat Output, Opt.
76        Generic data file
77
78

OTHER OPTIONS

80       -[no]hno
81        Print help info and quit
82
83       -[no]versionno
84        Print version info and quit
85
86       -nice int 19
87        Set the nicelevel
88
89       -b time 0
90        First frame (ps) to read from trajectory
91
92       -e time 0
93        Last frame (ps) to read from trajectory
94
95       -dt time 0
96        Only use frame when t MOD dt = first time (ps)
97
98       -[no]wno
99        View output xvg, xpm, eps and pdb files
100
101       -xvg enum xmgrace
102        xvg plot formatting:  xmgrace,  xmgr or  none
103
104       -nlevels int 40
105        Discretize rms in  levels
106
107       -max real -1
108        Maximum level in matrices
109
110       -[no]sumhyes
111        average distance over equivalent hydrogens
112
113       -[no]pbcyes
114        Use periodic boundary conditions when computing distances
115
116

NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO