1 .TH g_anaeig 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 g_anaeig - analyzes the eigenvectors
8 .BI "\-v" " eigenvec.trr "
9 .BI "\-v2" " eigenvec2.trr "
10 .BI "\-f" " traj.xtc "
11 .BI "\-s" " topol.tpr "
12 .BI "\-n" " index.ndx "
13 .BI "\-eig" " eigenval.xvg "
14 .BI "\-eig2" " eigenval2.xvg "
15 .BI "\-comp" " eigcomp.xvg "
16 .BI "\-rmsf" " eigrmsf.xvg "
17 .BI "\-proj" " proj.xvg "
18 .BI "\-2d" " 2dproj.xvg "
19 .BI "\-3d" " 3dproj.pdb "
20 .BI "\-filt" " filtered.xtc "
21 .BI "\-extr" " extreme.pdb "
22 .BI "\-over" " overlap.xvg "
23 .BI "\-inpr" " inprod.xpm "
25 .BI "\-[no]version" ""
37 .BI "\-nframes" " int "
39 .BI "\-[no]entropy" ""
41 .BI "\-nevskip" " int "
43 \&\fB g_anaeig\fR analyzes eigenvectors. The eigenvectors can be of a
44 \&covariance matrix (\fB g_covar\fR) or of a Normal Modes analysis
48 \&When a trajectory is projected on eigenvectors, all structures are
49 \&fitted to the structure in the eigenvector file, if present, otherwise
50 \&to the structure in the structure file. When no run input file is
51 \&supplied, periodicity will not be taken into account. Most analyses
52 \&are performed on eigenvectors \fB \-first\fR to \fB \-last\fR, but when
53 \&\fB \-first\fR is set to \-1 you will be prompted for a selection.
56 \&\fB \-comp\fR: plot the vector components per atom of eigenvectors
57 \&\fB \-first\fR to \fB \-last\fR.
60 \&\fB \-rmsf\fR: plot the RMS fluctuation per atom of eigenvectors
61 \&\fB \-first\fR to \fB \-last\fR (requires \fB \-eig\fR).
64 \&\fB \-proj\fR: calculate projections of a trajectory on eigenvectors
65 \&\fB \-first\fR to \fB \-last\fR.
66 \&The projections of a trajectory on the eigenvectors of its
67 \&covariance matrix are called principal components (pc's).
68 \&It is often useful to check the cosine content of the pc's,
69 \&since the pc's of random diffusion are cosines with the number
70 \&of periods equal to half the pc index.
71 \&The cosine content of the pc's can be calculated with the program
75 \&\fB \-2d\fR: calculate a 2d projection of a trajectory on eigenvectors
76 \&\fB \-first\fR and \fB \-last\fR.
79 \&\fB \-3d\fR: calculate a 3d projection of a trajectory on the first
80 \&three selected eigenvectors.
83 \&\fB \-filt\fR: filter the trajectory to show only the motion along
84 \&eigenvectors \fB \-first\fR to \fB \-last\fR.
87 \&\fB \-extr\fR: calculate the two extreme projections along a trajectory
88 \&on the average structure and interpolate \fB \-nframes\fR frames
89 \&between them, or set your own extremes with \fB \-max\fR. The
90 \&eigenvector \fB \-first\fR will be written unless \fB \-first\fR and
91 \&\fB \-last\fR have been set explicitly, in which case all eigenvectors
92 \&will be written to separate files. Chain identifiers will be added
93 \&when writing a \fB .pdb\fR file with two or three structures (you
94 \&can use \fB rasmol \-nmrpdb\fR to view such a pdb file).
97 \& Overlap calculations between covariance analysis:
99 \& NOTE: the analysis should use the same fitting structure
102 \&\fB \-over\fR: calculate the subspace overlap of the eigenvectors in
103 \&file \fB \-v2\fR with eigenvectors \fB \-first\fR to \fB \-last\fR
104 \&in file \fB \-v\fR.
107 \&\fB \-inpr\fR: calculate a matrix of inner\-products between
108 \&eigenvectors in files \fB \-v\fR and \fB \-v2\fR. All eigenvectors
109 \&of both files will be used unless \fB \-first\fR and \fB \-last\fR
110 \&have been set explicitly.
113 \&When \fB \-v\fR, \fB \-eig\fR, \fB \-v2\fR and \fB \-eig2\fR are given,
114 \&a single number for the overlap between the covariance matrices is
115 \&generated. The formulas are:
117 \& difference = sqrt(tr((sqrt(M1) \- sqrt(M2))2))
119 \&normalized overlap = 1 \- difference/sqrt(tr(M1) + tr(M2))
121 \& shape overlap = 1 \- sqrt(tr((sqrt(M1/tr(M1)) \- sqrt(M2/tr(M2)))2))
123 \&where M1 and M2 are the two covariance matrices and tr is the trace
124 \&of a matrix. The numbers are proportional to the overlap of the square
125 \&root of the fluctuations. The normalized overlap is the most useful
126 \&number, it is 1 for identical matrices and 0 when the sampled
127 \&subspaces are orthogonal.
130 \&When the \fB \-entropy\fR flag is given an entropy estimate will be
131 \&computed based on the Quasiharmonic approach and based on
132 \&Schlitter's formula.
134 .BI "\-v" " eigenvec.trr"
136 Full precision trajectory: trr trj cpt
138 .BI "\-v2" " eigenvec2.trr"
140 Full precision trajectory: trr trj cpt
142 .BI "\-f" " traj.xtc"
144 Trajectory: xtc trr trj gro g96 pdb cpt
146 .BI "\-s" " topol.tpr"
148 Structure+mass(db): tpr tpb tpa gro g96 pdb
150 .BI "\-n" " index.ndx"
154 .BI "\-eig" " eigenval.xvg"
158 .BI "\-eig2" " eigenval2.xvg"
162 .BI "\-comp" " eigcomp.xvg"
166 .BI "\-rmsf" " eigrmsf.xvg"
170 .BI "\-proj" " proj.xvg"
174 .BI "\-2d" " 2dproj.xvg"
178 .BI "\-3d" " 3dproj.pdb"
180 Structure file: gro g96 pdb etc.
182 .BI "\-filt" " filtered.xtc"
184 Trajectory: xtc trr trj gro g96 pdb cpt
186 .BI "\-extr" " extreme.pdb"
188 Trajectory: xtc trr trj gro g96 pdb cpt
190 .BI "\-over" " overlap.xvg"
194 .BI "\-inpr" " inprod.xpm"
196 X PixMap compatible matrix file
200 Print help info and quit
202 .BI "\-[no]version" "no "
203 Print version info and quit
205 .BI "\-nice" " int" " 19"
208 .BI "\-b" " time" " 0 "
209 First frame (ps) to read from trajectory
211 .BI "\-e" " time" " 0 "
212 Last frame (ps) to read from trajectory
214 .BI "\-dt" " time" " 0 "
215 Only use frame when t MOD dt = first time (ps)
217 .BI "\-tu" " enum" " ps"
218 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR
221 View output xvg, xpm, eps and pdb files
223 .BI "\-xvg" " enum" " xmgrace"
224 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
226 .BI "\-first" " int" " 1"
227 First eigenvector for analysis (\-1 is select)
229 .BI "\-last" " int" " 8"
230 Last eigenvector for analysis (\-1 is till the last)
232 .BI "\-skip" " int" " 1"
233 Only analyse every nr\-th frame
235 .BI "\-max" " real" " 0 "
236 Maximum for projection of the eigenvector on the average structure, max=0 gives the extremes
238 .BI "\-nframes" " int" " 2"
239 Number of frames for the extremes output
241 .BI "\-[no]split" "no "
242 Split eigenvector projections where time is zero
244 .BI "\-[no]entropy" "no "
245 Compute entropy according to the Quasiharmonic formula or Schlitter's method.
247 .BI "\-temp" " real" " 298.15"
248 Temperature for entropy calculations
250 .BI "\-nevskip" " int" " 6"
251 Number of eigenvalues to skip when computing the entropy due to the quasi harmonic approximation. When you do a rotational and/or translational fit prior to the covariance analysis, you get 3 or 6 eigenvalues that are very close to zero, and which should not be taken into account when computing the entropy.
256 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.