g_anaeig(1)

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

6       g_anaeig - analyzes the eigenvectors
7
8       VERSION 4.5
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SYNOPSIS

11       g_anaeig  -v eigenvec.trr -v2 eigenvec2.trr -f traj.xtc -s topol.tpr -n
12       index.ndx -eig eigenval.xvg -eig2 eigenval2.xvg -comp eigcomp.xvg -rmsf
13       eigrmsf.xvg  -proj  proj.xvg  -2d  2dproj.xvg -3d 3dproj.pdb -filt fil‐
14       tered.xtc -extr extreme.pdb -over overlap.xvg -inpr  inprod.xpm  -[no]h
15       -[no]version  -nice  int  -b time -e time -dt time -tu enum -[no]w -xvg
16       enum -first int -last int -skip int -max real -nframes  int  -[no]split
17       -[no]entropy -temp real -nevskip int
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DESCRIPTION

20         g_anaeig  analyzes eigenvectors. The eigenvectors can be of a covari‐
21       ance matrix ( g_covar) or of a Normal Modes analysis ( g_nmeig).
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24       When a trajectory is projected on eigenvectors, all structures are fit‐
25       ted  to the structure in the eigenvector file, if present, otherwise to
26       the structure in the structure file. When no run  input  file  is  sup‐
27       plied,  periodicity  will  not be taken into account. Most analyses are
28       performed on eigenvectors  -first to  -last, but when  -first is set to
29       -1 you will be prompted for a selection.
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31
32         -comp: plot the vector components per atom of eigenvectors  -first to
33       -last.
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35
36        -rmsf: plot the RMS fluctuation per atom of eigenvectors    -first  to
37       -last (requires  -eig).
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40         -proj:  calculate projections of a trajectory on eigenvectors  -first
41       to  -last.  The projections of a trajectory on the eigenvectors of  its
42       covariance  matrix are called principal components (pc's).  It is often
43       useful to check the cosine content of the pc's, since the pc's of  ran‐
44       dom  diffusion are cosines with the number of periods equal to half the
45       pc index.  The cosine content of the pc's can be  calculated  with  the
46       program  g_analyze.
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49        -2d: calculate a 2d projection of a trajectory on eigenvectors  -first
50       and  -last.
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53        -3d: calculate a 3d projection of a  trajectory  on  the  first  three
54       selected eigenvectors.
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57         -filt:  filter the trajectory to show only the motion along eigenvec‐
58       tors  -first to  -last.
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61        -extr: calculate the two extreme projections along a trajectory on the
62       average structure and interpolate  -nframes frames between them, or set
63       your own extremes with  -max. The eigenvector  -first will  be  written
64       unless   -first  and  -last have been set explicitly, in which case all
65       eigenvectors will be written to separate files. Chain identifiers  will
66       be  added  when  writing a  .pdb file with two or three structures (you
67       can use  rasmol -nmrpdb to view such a pdb file).
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69
70         Overlap calculations between covariance analysis:
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72         NOTE: the analysis should use the same fitting structure
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75        -over: calculate the subspace overlap of the eigenvectors in file  -v2
76       with eigenvectors  -first to  -last in file  -v.
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79         -inpr:  calculate  a matrix of inner-products between eigenvectors in
80       files  -v and  -v2. All eigenvectors of both files will be used  unless
81       -first and  -last have been set explicitly.
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83
84       When   -v,   -eig,   -v2  and  -eig2 are given, a single number for the
85       overlap between the covariance matrices is generated. The formulas are:
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87               difference = sqrt(tr((sqrt(M1) - sqrt(M2))2))
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89       normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))
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91            shape overlap = 1 - sqrt(tr((sqrt(M1/tr(M1)) - sqrt(M2/tr(M2)))2))
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93       where M1 and M2 are the two covariance matrices and tr is the trace  of
94       a  matrix.  The  numbers  are proportional to the overlap of the square
95       root of the fluctuations. The normalized overlap  is  the  most  useful
96       number, it is 1 for identical matrices and 0 when the sampled subspaces
97       are orthogonal.
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100       When the  -entropy flag is given an entropy estimate will  be  computed
101       based on the Quasiharmonic approach and based on Schlitter's formula.
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FILES

104       -v eigenvec.trr Input
105        Full precision trajectory: trr trj cpt
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107       -v2 eigenvec2.trr Input, Opt.
108        Full precision trajectory: trr trj cpt
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110       -f traj.xtc Input, Opt.
111        Trajectory: xtc trr trj gro g96 pdb cpt
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113       -s topol.tpr Input, Opt.
114        Structure+mass(db): tpr tpb tpa gro g96 pdb
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116       -n index.ndx Input, Opt.
117        Index file
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119       -eig eigenval.xvg Input, Opt.
120        xvgr/xmgr file
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122       -eig2 eigenval2.xvg Input, Opt.
123        xvgr/xmgr file
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125       -comp eigcomp.xvg Output, Opt.
126        xvgr/xmgr file
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128       -rmsf eigrmsf.xvg Output, Opt.
129        xvgr/xmgr file
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131       -proj proj.xvg Output, Opt.
132        xvgr/xmgr file
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134       -2d 2dproj.xvg Output, Opt.
135        xvgr/xmgr file
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137       -3d 3dproj.pdb Output, Opt.
138        Structure file: gro g96 pdb etc.
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140       -filt filtered.xtc Output, Opt.
141        Trajectory: xtc trr trj gro g96 pdb cpt
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143       -extr extreme.pdb Output, Opt.
144        Trajectory: xtc trr trj gro g96 pdb cpt
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146       -over overlap.xvg Output, Opt.
147        xvgr/xmgr file
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149       -inpr inprod.xpm Output, Opt.
150        X PixMap compatible matrix file
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OTHER OPTIONS

154       -[no]hno
155        Print help info and quit
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157       -[no]versionno
158        Print version info and quit
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160       -nice int 19
161        Set the nicelevel
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163       -b time 0
164        First frame (ps) to read from trajectory
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166       -e time 0
167        Last frame (ps) to read from trajectory
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169       -dt time 0
170        Only use frame when t MOD dt = first time (ps)
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172       -tu enum ps
173        Time unit:  fs,  ps,  ns,  us,  ms or  s
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175       -[no]wno
176        View output xvg, xpm, eps and pdb files
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178       -xvg enum xmgrace
179        xvg plot formatting:  xmgrace,  xmgr or  none
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181       -first int 1
182        First eigenvector for analysis (-1 is select)
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184       -last int 8
185        Last eigenvector for analysis (-1 is till the last)
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187       -skip int 1
188        Only analyse every nr-th frame
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190       -max real 0
191        Maximum  for  projection  of the eigenvector on the average structure,
192       max=0 gives the extremes
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194       -nframes int 2
195        Number of frames for the extremes output
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197       -[no]splitno
198        Split eigenvector projections where time is zero
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200       -[no]entropyno
201        Compute entropy according to the Quasiharmonic formula or  Schlitter's
202       method.
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204       -temp real 298.15
205        Temperature for entropy calculations
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207       -nevskip int 6
208        Number  of  eigenvalues  to skip when computing the entropy due to the
209       quasi harmonic approximation. When you do a rotational and/or  transla‐
210       tional fit prior to the covariance analysis, you get 3 or 6 eigenvalues
211       that are very close to zero, and which should not be taken into account
212       when computing the entropy.
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO