1GMX-RMS(1)                          GROMACS                         GMX-RMS(1)
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NAME

6       gmx-rms - Calculate RMSDs with a reference structure and RMSD matrices
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SYNOPSIS

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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DESCRIPTION

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.
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25       Each structure from a trajectory (-f) is compared to a reference struc‐
26       ture. The reference structure is taken from the structure file (-s).
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28       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).
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32       Option  -prev  produces the comparison with a previous frame the speci‐
33       fied number of frames ago.
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35       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.
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40       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.
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44       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.
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52       With  -f2,  the  ‘other structures’ are taken from a second trajectory,
53       this generates a comparison matrix of one trajectory versus the other.
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55       Option -bin does a binary dump of the comparison matrix.
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57       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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OPTIONS

62       Options to specify input files:
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64       -s [<.tpr/.gro/…>] (topol.tpr)
65              Structure+mass(db): tpr gro g96 pdb brk ent
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67       -f [<.xtc/.trr/…>] (traj.xtc)
68              Trajectory: xtc trr cpt gro g96 pdb tng
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70       -f2 [<.xtc/.trr/…>] (traj.xtc) (Optional)
71              Trajectory: xtc trr cpt gro g96 pdb tng
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73       -n [<.ndx>] (index.ndx) (Optional)
74              Index file
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76       Options to specify output files:
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78       -o [<.xvg>] (rmsd.xvg)
79              xvgr/xmgr file
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81       -mir [<.xvg>] (rmsdmir.xvg) (Optional)
82              xvgr/xmgr file
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84       -a [<.xvg>] (avgrp.xvg) (Optional)
85              xvgr/xmgr file
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87       -dist [<.xvg>] (rmsd-dist.xvg) (Optional)
88              xvgr/xmgr file
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90       -m [<.xpm>] (rmsd.xpm) (Optional)
91              X PixMap compatible matrix file
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93       -bin [<.dat>] (rmsd.dat) (Optional)
94              Generic data file
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96       -bm [<.xpm>] (bond.xpm) (Optional)
97              X PixMap compatible matrix file
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99       Other options:
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101       -b <time> (0)
102              Time of first frame to read from trajectory (default unit ps)
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104       -e <time> (0)
105              Time of last frame to read from trajectory (default unit ps)
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107       -dt <time> (0)
108              Only use frame when t MOD dt = first time (default unit ps)
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110       -tu <enum> (ps)
111              Unit for time values: fs, ps, ns, us, ms, s
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113       -[no]w (no)
114              View output .xvg, .xpm, .eps and .pdb files
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116       -xvg <enum> (xmgrace)
117              xvg plot formatting: xmgrace, xmgr, none
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119       -what <enum> (rmsd)
120              Structural difference measure: rmsd, rho, rhosc
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122       -[no]pbc (yes)
123              PBC check
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125       -fit <enum> (rot+trans)
126              Fit to reference structure: rot+trans, translation, none
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128       -prev <int> (0)
129              Compare with previous frame
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131       -[no]split (no)
132              Split graph where time is zero
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134       -skip <int> (1)
135              Only write every nr-th frame to matrix
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137       -skip2 <int> (1)
138              Only write every nr-th frame to matrix
139
140       -max <real> (-1)
141              Maximum level in comparison matrix
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143       -min <real> (-1)
144              Minimum level in comparison matrix
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146       -bmax <real> (-1)
147              Maximum level in bond angle matrix
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149       -bmin <real> (-1)
150              Minimum level in bond angle matrix
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152       -[no]mw (yes)
153              Use mass weighting for superposition
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155       -nlevels <int> (80)
156              Number of levels in the matrices
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158       -ng <int> (1)
159              Number of groups to compute RMS between
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SEE ALSO

162       gmx(1)
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164       More    information    about    GROMACS    is    available    at     <‐
165       http://www.gromacs.org/>.
166
168       2020, GROMACS development team
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1732019.6                           Feb 28, 2020                       GMX-RMS(1)
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