g_rms(1) - f14

1g_rms(1)                  GROMACS suite, VERSION 4.5                  g_rms(1)
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NAME

6       g_rms - calculates rmsd's with a reference structure and rmsd matrices
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8       VERSION 4.5
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SYNOPSIS

11       g_rms  -s  topol.tpr  -f traj.xtc -f2 traj.xtc -n index.ndx -o rmsd.xvg
12       -mir rmsdmir.xvg -a avgrp.xvg  -dist  rmsd-dist.xvg  -m  rmsd.xpm  -bin
13       rmsd.dat -bm bond.xpm -[no]h -[no]version -nice int -b time -e time -dt
14       time -tu enum -[no]w -xvg enum -what enum -[no]pbc -fit enum -prev  int
15       -[no]split  -skip  int  -skip2 int -max real -min real -bmax real -bmin
16       real -[no]mw -nlevels int -ng int
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DESCRIPTION

19       g_rms compares two structures by computing the root mean square  devia‐
20       tion  (RMSD),  the size-independent 'rho' similarity parameter (rho) or
21       the scaled rho (rhosc),  see  Maiorov  &  Crippen,  PROTEINS   22,  273
22       (1995).  This is selected by  -what.
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24       Each  structure  from  a  trajectory  (  -f) is compared to a reference
25       structure. The reference structure is taken from the structure  file  (
26       -s).
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29       With option  -mir also a comparison with the mirror image of the refer‐
30       ence structure is calculated.  This is useful as a reference for  'sig‐
31       nificant' values, see Maiorov & Crippen, PROTEINS  22, 273 (1995).
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34       Option   -prev produces the comparison with a previous frame the speci‐
35       fied number of frames ago.
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38       Option  -m produces a matrix in  .xpm format of  comparison  values  of
39       each  structure in the trajectory with respect to each other structure.
40       This file can be visualized with for instance  xv and can be  converted
41       to postscript with  xpm2ps.
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44       Option   -fit  controls  the least-squares fitting of the structures on
45       top of each other: complete fit (rotation and translation), translation
46       only, or no fitting at all.
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49       Option   -mw  controls  whether  mass weighting is done or not.  If you
50       select the option (default) and supply a valid tpr file masses will  be
51       taken  from  there, otherwise the masses will be deduced from the atom‐
52       mass.dat file in the GROMACS library directory. This is fine  for  pro‐
53       teins but not necessarily for other molecules. A default mass of 12.011
54       amu (Carbon) is assigned to unknown atoms. You can check  whether  this
55       happend by turning on the  -debug flag and inspecting the log file.
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58       With   -f2,  the 'other structures' are taken from a second trajectory,
59       this generates a comparison matrix of one trajectory versus the other.
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62       Option  -bin does a binary dump of the comparison matrix.
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65       Option  -bm produces a matrix of average bond angle  deviations  analo‐
66       gously  to  the   -m option. Only bonds between atoms in the comparison
67       group are considered.
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FILES

70       -s topol.tpr Input
71        Structure+mass(db): tpr tpb tpa gro g96 pdb
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73       -f traj.xtc Input
74        Trajectory: xtc trr trj gro g96 pdb cpt
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76       -f2 traj.xtc Input, Opt.
77        Trajectory: xtc trr trj gro g96 pdb cpt
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79       -n index.ndx Input, Opt.
80        Index file
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82       -o rmsd.xvg Output
83        xvgr/xmgr file
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85       -mir rmsdmir.xvg Output, Opt.
86        xvgr/xmgr file
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88       -a avgrp.xvg Output, Opt.
89        xvgr/xmgr file
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91       -dist rmsd-dist.xvg Output, Opt.
92        xvgr/xmgr file
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94       -m rmsd.xpm Output, Opt.
95        X PixMap compatible matrix file
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97       -bin rmsd.dat Output, Opt.
98        Generic data file
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100       -bm bond.xpm Output, Opt.
101        X PixMap compatible matrix file
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OTHER OPTIONS

105       -[no]hno
106        Print help info and quit
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108       -[no]versionno
109        Print version info and quit
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111       -nice int 19
112        Set the nicelevel
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114       -b time 0
115        First frame (ps) to read from trajectory
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117       -e time 0
118        Last frame (ps) to read from trajectory
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120       -dt time 0
121        Only use frame when t MOD dt = first time (ps)
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123       -tu enum ps
124        Time unit:  fs,  ps,  ns,  us,  ms or  s
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126       -[no]wno
127        View output xvg, xpm, eps and pdb files
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129       -xvg enum xmgrace
130        xvg plot formatting:  xmgrace,  xmgr or  none
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132       -what enum rmsd
133        Structural difference measure:  rmsd,  rho or  rhosc
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135       -[no]pbcyes
136        PBC check
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138       -fit enum rot+trans
139        Fit to reference structure:  rot+trans,  translation or  none
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141       -prev int 0
142        Compare with previous frame
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144       -[no]splitno
145        Split graph where time is zero
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147       -skip int 1
148        Only write every nr-th frame to matrix
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150       -skip2 int 1
151        Only write every nr-th frame to matrix
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153       -max real -1
154        Maximum level in comparison matrix
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156       -min real -1
157        Minimum level in comparison matrix
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159       -bmax real -1
160        Maximum level in bond angle matrix
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162       -bmin real -1
163        Minimum level in bond angle matrix
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165       -[no]mwyes
166        Use mass weighting for superposition
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168       -nlevels int 80
169        Number of levels in the matrices
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171       -ng int 1
172        Number of groups to compute RMS between
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO