1 .TH g_rms 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 g_rms - calculates rmsd's with a reference structure and rmsd matrices
8 .BI "\-s" " topol.tpr "
10 .BI "\-f2" " traj.xtc "
11 .BI "\-n" " index.ndx "
12 .BI "\-o" " rmsd.xvg "
13 .BI "\-mir" " rmsdmir.xvg "
14 .BI "\-a" " avgrp.xvg "
15 .BI "\-dist" " rmsd\-dist.xvg "
16 .BI "\-m" " rmsd.xpm "
17 .BI "\-bin" " rmsd.dat "
18 .BI "\-bm" " bond.xpm "
20 .BI "\-[no]version" ""
40 .BI "\-nlevels" " int "
43 \&g_rms compares two structures by computing the root mean square
44 \&deviation (RMSD), the size\-independent 'rho' similarity parameter
45 \&(rho) or the scaled rho (rhosc),
46 \&see Maiorov & Crippen, PROTEINS \fB 22\fR, 273 (1995).
47 \&This is selected by \fB \-what\fR.
49 Each structure from a trajectory (\fB \-f\fR) is compared to a
50 \&reference structure. The reference structure
51 \&is taken from the structure file (\fB \-s\fR).
54 \&With option \fB \-mir\fR also a comparison with the mirror image of
55 \&the reference structure is calculated.
56 \&This is useful as a reference for 'significant' values, see
57 \&Maiorov & Crippen, PROTEINS \fB 22\fR, 273 (1995).
60 \&Option \fB \-prev\fR produces the comparison with a previous frame
61 \&the specified number of frames ago.
64 \&Option \fB \-m\fR produces a matrix in \fB .xpm\fR format of
65 \&comparison values of each structure in the trajectory with respect to
66 \&each other structure. This file can be visualized with for instance
67 \&\fB xv\fR and can be converted to postscript with \fB xpm2ps\fR.
70 \&Option \fB \-fit\fR controls the least\-squares fitting of
71 \&the structures on top of each other: complete fit (rotation and
72 \&translation), translation only, or no fitting at all.
75 \&Option \fB \-mw\fR controls whether mass weighting is done or not.
76 \&If you select the option (default) and
77 \&supply a valid tpr file masses will be taken from there,
78 \&otherwise the masses will be deduced from the atommass.dat file in
79 \&the GROMACS library directory. This is fine for proteins but not
80 \&necessarily for other molecules. A default mass of 12.011 amu (Carbon)
81 \&is assigned to unknown atoms. You can check whether this happend by
82 \&turning on the \fB \-debug\fR flag and inspecting the log file.
85 \&With \fB \-f2\fR, the 'other structures' are taken from a second
86 \&trajectory, this generates a comparison matrix of one trajectory
90 \&Option \fB \-bin\fR does a binary dump of the comparison matrix.
93 \&Option \fB \-bm\fR produces a matrix of average bond angle deviations
94 \&analogously to the \fB \-m\fR option. Only bonds between atoms in the
95 \&comparison group are considered.
97 .BI "\-s" " topol.tpr"
99 Structure+mass(db): tpr tpb tpa gro g96 pdb
101 .BI "\-f" " traj.xtc"
103 Trajectory: xtc trr trj gro g96 pdb cpt
105 .BI "\-f2" " traj.xtc"
107 Trajectory: xtc trr trj gro g96 pdb cpt
109 .BI "\-n" " index.ndx"
113 .BI "\-o" " rmsd.xvg"
117 .BI "\-mir" " rmsdmir.xvg"
121 .BI "\-a" " avgrp.xvg"
125 .BI "\-dist" " rmsd\-dist.xvg"
129 .BI "\-m" " rmsd.xpm"
131 X PixMap compatible matrix file
133 .BI "\-bin" " rmsd.dat"
137 .BI "\-bm" " bond.xpm"
139 X PixMap compatible matrix file
143 Print help info and quit
145 .BI "\-[no]version" "no "
146 Print version info and quit
148 .BI "\-nice" " int" " 19"
151 .BI "\-b" " time" " 0 "
152 First frame (ps) to read from trajectory
154 .BI "\-e" " time" " 0 "
155 Last frame (ps) to read from trajectory
157 .BI "\-dt" " time" " 0 "
158 Only use frame when t MOD dt = first time (ps)
160 .BI "\-tu" " enum" " ps"
161 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR
164 View output xvg, xpm, eps and pdb files
166 .BI "\-xvg" " enum" " xmgrace"
167 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
169 .BI "\-what" " enum" " rmsd"
170 Structural difference measure: \fB rmsd\fR, \fB rho\fR or \fB rhosc\fR
172 .BI "\-[no]pbc" "yes "
175 .BI "\-fit" " enum" " rot+trans"
176 Fit to reference structure: \fB rot+trans\fR, \fB translation\fR or \fB none\fR
178 .BI "\-prev" " int" " 0"
179 Compare with previous frame
181 .BI "\-[no]split" "no "
182 Split graph where time is zero
184 .BI "\-skip" " int" " 1"
185 Only write every nr\-th frame to matrix
187 .BI "\-skip2" " int" " 1"
188 Only write every nr\-th frame to matrix
190 .BI "\-max" " real" " \-1 "
191 Maximum level in comparison matrix
193 .BI "\-min" " real" " \-1 "
194 Minimum level in comparison matrix
196 .BI "\-bmax" " real" " \-1 "
197 Maximum level in bond angle matrix
199 .BI "\-bmin" " real" " \-1 "
200 Minimum level in bond angle matrix
202 .BI "\-[no]mw" "yes "
203 Use mass weighting for superposition
205 .BI "\-nlevels" " int" " 80"
206 Number of levels in the matrices
208 .BI "\-ng" " int" " 1"
209 Number of groups to compute RMS between
214 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.