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 se‐
45 lect 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 (deprecated). This is fine for proteins, but
48 not necessarily for other molecules. You can check whether this hap‐
49 pened by turning on the -debug flag and inspecting the log file.
50 With -f2, the 'other structures' are taken from a second trajectory,
52 this generates a comparison matrix of one trajectory versus the other.
53 Option -bin does a binary dump of the comparison matrix.
55 Option -bm produces a matrix of average bond angle deviations analo‐
57 gously to the -m option. Only bonds between atoms in the comparison
58 group are considered.
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61 Options to specify input files:
62 -s [<.tpr/.gro/...>] (topol.tpr)
64 Structure+mass(db): tpr gro g96 pdb brk ent
65 -f [<.xtc/.trr/...>] (traj.xtc)
67 Trajectory: xtc trr cpt gro g96 pdb tng
68 -f2 [<.xtc/.trr/...>] (traj.xtc) (Optional)
70 Trajectory: xtc trr cpt gro g96 pdb tng
71 -n [<.ndx>] (index.ndx) (Optional)
73 Index file
74 Options to specify output files:
76 -o [<.xvg>] (rmsd.xvg)
78 xvgr/xmgr file
79 -mir [<.xvg>] (rmsdmir.xvg) (Optional)
81 xvgr/xmgr file
82 -a [<.xvg>] (avgrp.xvg) (Optional)
84 xvgr/xmgr file
85 -dist [<.xvg>] (rmsd-dist.xvg) (Optional)
87 xvgr/xmgr file
88 -m [<.xpm>] (rmsd.xpm) (Optional)
90 X PixMap compatible matrix file
91 -bin [<.dat>] (rmsd.dat) (Optional)
93 Generic data file
94 -bm [<.xpm>] (bond.xpm) (Optional)
96 X PixMap compatible matrix file
97 Other options:
99 -b <time> (0)
101 Time of first frame to read from trajectory (default unit ps)
102 -e <time> (0)
104 Time of last frame to read from trajectory (default unit ps)
105 -dt <time> (0)
107 Only use frame when t MOD dt = first time (default unit ps)
108 -tu <enum> (ps)
110 Unit for time values: fs, ps, ns, us, ms, s
111 -[no]w (no)
113 View output .xvg, .xpm, .eps and .pdb files
114 -xvg <enum> (xmgrace)
116 xvg plot formatting: xmgrace, xmgr, none
117 -what <enum> (rmsd)
119 Structural difference measure: rmsd, rho, rhosc
120 -[no]pbc (yes)
122 PBC check
123 -fit <enum> (rot+trans)
125 Fit to reference structure: rot+trans, translation, none
126 -prev <int> (0)
128 Compare with previous frame
129 -[no]split (no)
131 Split graph where time is zero
132 -skip <int> (1)
134 Only write every nr-th frame to matrix
135 -skip2 <int> (1)
137 Only write every nr-th frame to matrix
138 -max <real> (-1)
140 Maximum level in comparison matrix
141 -min <real> (-1)
143 Minimum level in comparison matrix
144 -bmax <real> (-1)
146 Maximum level in bond angle matrix
147 -bmin <real> (-1)
149 Minimum level in bond angle matrix
150 -[no]mw (yes)
152 Use mass weighting for superposition
153 -nlevels <int> (80)
155 Number of levels in the matrices
156 -ng <int> (1)
158 Number of groups to compute RMS between
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161 gmx(1)
162 More information about GROMACS is available at <‐
164 http://www.gromacs.org/>.
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167 2022, GROMACS development team
1682022.3 Sep 02, 2022 GMX-RMS(1)