1GMX-RMS(1) GROMACS GMX-RMS(1)
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6 gmx-rms - Calculate RMSDs with a reference structure and RMSD matrices
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9 gmx rms [-s [<.tpr/.gro/...>]] [-f [<.xtc/.trr/...>]]
10 [-f2 [<.xtc/.trr/...>]] [-n [<.ndx>]] [-o [<.xvg>]]
11 [-mir [<.xvg>]] [-a [<.xvg>]] [-dist [<.xvg>]] [-m [<.xpm>]]
12 [-bin [<.dat>]] [-bm [<.xpm>]] [-b <time>] [-e <time>]
13 [-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
14 [-what <enum>] [-[no]pbc] [-fit <enum>] [-prev <int>]
15 [-[no]split] [-skip <int>] [-skip2 <int>] [-max <real>]
16 [-min <real>] [-bmax <real>] [-bmin <real>] [-[no]mw]
17 [-nlevels <int>] [-ng <int>]
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20 gmx rms compares two structures by computing the root mean square devi‐
21 ation (RMSD), the size-independent rho similarity parameter (rho) or
22 the scaled rho (rhosc), see Maiorov & Crippen, Proteins 22, 273 (1995).
23 This is selected by -what.
24 Each structure from a trajectory (-f) is compared to a reference struc‐
26 ture. The reference structure is taken from the structure file (-s).
27 With option -mir also a comparison with the mirror image of the refer‐
29 ence structure is calculated. This is useful as a reference for ‘sig‐
30 nificant’ values, see Maiorov & Crippen, Proteins 22, 273 (1995).
31 Option -prev produces the comparison with a previous frame the speci‐
33 fied number of frames ago.
34 Option -m produces a matrix in .xpm format of comparison values of each
36 structure in the trajectory with respect to each other structure. This
37 file can be visualized with for instance xv and can be converted to
38 postscript with gmx xpm2ps.
39 Option -fit controls the least-squares fitting of the structures on top
41 of each other: complete fit (rotation and translation), translation
42 only, or no fitting at all.
43 Option -mw controls whether mass weighting is done or not. If you
45 select the option (default) and supply a valid .tpr file masses will be
46 taken from there, otherwise the masses will be deduced from the atom‐
47 mass.dat file in GMXLIB. This is fine for proteins, but not necessarily
48 for other molecules. A default mass of 12.011 amu (carbon) is assigned
49 to unknown atoms. You can check whether this happened by turning on the
50 -debug flag and inspecting the log file.
51 With -f2, the ‘other structures’ are taken from a second trajectory,
53 this generates a comparison matrix of one trajectory versus the other.
54 Option -bin does a binary dump of the comparison matrix.
56 Option -bm produces a matrix of average bond angle deviations analo‐
58 gously to the -m option. Only bonds between atoms in the comparison
59 group are considered.
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62 Options to specify input files:
63 -s [<.tpr/.gro/…>] (topol.tpr)
65 Structure+mass(db): tpr gro g96 pdb brk ent
66 -f [<.xtc/.trr/…>] (traj.xtc)
68 Trajectory: xtc trr cpt gro g96 pdb tng
69 -f2 [<.xtc/.trr/…>] (traj.xtc) (Optional)
71 Trajectory: xtc trr cpt gro g96 pdb tng
72 -n [<.ndx>] (index.ndx) (Optional)
74 Index file
75 Options to specify output files:
77 -o [<.xvg>] (rmsd.xvg)
79 xvgr/xmgr file
80 -mir [<.xvg>] (rmsdmir.xvg) (Optional)
82 xvgr/xmgr file
83 -a [<.xvg>] (avgrp.xvg) (Optional)
85 xvgr/xmgr file
86 -dist [<.xvg>] (rmsd-dist.xvg) (Optional)
88 xvgr/xmgr file
89 -m [<.xpm>] (rmsd.xpm) (Optional)
91 X PixMap compatible matrix file
92 -bin [<.dat>] (rmsd.dat) (Optional)
94 Generic data file
95 -bm [<.xpm>] (bond.xpm) (Optional)
97 X PixMap compatible matrix file
98 Other options:
100 -b <time> (0)
102 Time of first frame to read from trajectory (default unit ps)
103 -e <time> (0)
105 Time of last frame to read from trajectory (default unit ps)
106 -dt <time> (0)
108 Only use frame when t MOD dt = first time (default unit ps)
109 -tu <enum> (ps)
111 Unit for time values: fs, ps, ns, us, ms, s
112 -[no]w (no)
114 View output .xvg, .xpm, .eps and .pdb files
115 -xvg <enum> (xmgrace)
117 xvg plot formatting: xmgrace, xmgr, none
118 -what <enum> (rmsd)
120 Structural difference measure: rmsd, rho, rhosc
121 -[no]pbc (yes)
123 PBC check
124 -fit <enum> (rot+trans)
126 Fit to reference structure: rot+trans, translation, none
127 -prev <int> (0)
129 Compare with previous frame
130 -[no]split (no)
132 Split graph where time is zero
133 -skip <int> (1)
135 Only write every nr-th frame to matrix
136 -skip2 <int> (1)
138 Only write every nr-th frame to matrix
139 -max <real> (-1)
141 Maximum level in comparison matrix
142 -min <real> (-1)
144 Minimum level in comparison matrix
145 -bmax <real> (-1)
147 Maximum level in bond angle matrix
148 -bmin <real> (-1)
150 Minimum level in bond angle matrix
151 -[no]mw (yes)
153 Use mass weighting for superposition
154 -nlevels <int> (80)
156 Number of levels in the matrices
157 -ng <int> (1)
159 Number of groups to compute RMS between
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162 gmx(1)
163 More information about GROMACS is available at <‐
165 http://www.gromacs.org/>.
166
168 2019, GROMACS development team
1692018.7 May 29, 2019 GMX-RMS(1)