1GMX-ANAEIG(1) GROMACS GMX-ANAEIG(1)
2
6 gmx-anaeig - Analyze eigenvectors/normal modes
7
9 gmx anaeig [-v [<.trr/.cpt/...>]] [-v2 [<.trr/.cpt/...>]]
10 [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
11 [-n [<.ndx>]] [-eig [<.xvg>]] [-eig2 [<.xvg>]]
12 [-comp [<.xvg>]] [-rmsf [<.xvg>]] [-proj [<.xvg>]]
13 [-2d [<.xvg>]] [-3d [<.gro/.g96/...>]]
14 [-filt [<.xtc/.trr/...>]] [-extr [<.xtc/.trr/...>]]
15 [-over [<.xvg>]] [-inpr [<.xpm>]] [-b <time>] [-e <time>]
16 [-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
17 [-first <int>] [-last <int>] [-skip <int>] [-max <real>]
18 [-nframes <int>] [-[no]split] [-[no]entropy]
19 [-temp <real>] [-nevskip <int>]
20
22 gmx anaeig analyzes eigenvectors. The eigenvectors can be of a covari‐
23 ance matrix (gmx covar) or of a Normal Modes analysis (gmx nmeig).
24 When a trajectory is projected on eigenvectors, all structures are fit‐
26 ted to the structure in the eigenvector file, if present, otherwise to
27 the structure in the structure file. When no run input file is sup‐
28 plied, periodicity will not be taken into account. Most analyses are
29 performed on eigenvectors -first to -last, but when -first is set to -1
30 you will be prompted for a selection.
31 -comp: plot the vector components per atom of eigenvectors -first to
33 -last.
34 -rmsf: plot the RMS fluctuation per atom of eigenvectors -first to
36 -last (requires -eig).
37 -proj: calculate projections of a trajectory on eigenvectors -first to
39 -last. The projections of a trajectory on the eigenvectors of its co‐
40 variance matrix are called principal components (pc's). It is often
41 useful to check the cosine content of the pc's, since the pc's of ran‐
42 dom diffusion are cosines with the number of periods equal to half the
43 pc index. The cosine content of the pc's can be calculated with the
44 program gmx analyze.
45 -2d: calculate a 2d projection of a trajectory on eigenvectors -first
47 and -last.
48 -3d: calculate a 3d projection of a trajectory on the first three se‐
50 lected eigenvectors.
51 -filt: filter the trajectory to show only the motion along eigenvectors
53 -first to -last.
54 -extr: calculate the two extreme projections along a trajectory on the
56 average structure and interpolate -nframes frames between them, or set
57 your own extremes with -max. The eigenvector -first will be written un‐
58 less -first and -last have been set explicitly, in which case all
59 eigenvectors will be written to separate files. Chain identifiers will
60 be added when writing a .pdb file with two or three structures (you can
61 use rasmol -nmrpdb to view such a .pdb file).
62 Overlap calculations between covariance analysis
64 Note: the analysis should use the same fitting structure
65 -over: calculate the subspace overlap of the eigenvectors in file -v2
67 with eigenvectors -first to -last in file -v.
68 -inpr: calculate a matrix of inner-products between eigenvectors in
70 files -v and -v2. All eigenvectors of both files will be used unless
71 -first and -last have been set explicitly.
72 When -v and -v2 are given, a single number for the overlap between the
74 covariance matrices is generated. Note that the eigenvalues are by de‐
75 fault read from the timestamp field in the eigenvector input files, but
76 when -eig, or -eig2 are given, the corresponding eigenvalues are used
77 instead. The formulas are:
78 difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2))
80 normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))
81 shape overlap = 1 - sqrt(tr((sqrt(M1/tr(M1)) - sqrt(M2/tr(M2)))^2))
82 where M1 and M2 are the two covariance matrices and tr is the trace of
84 a matrix. The numbers are proportional to the overlap of the square
85 root of the fluctuations. The normalized overlap is the most useful
86 number, it is 1 for identical matrices and 0 when the sampled subspaces
87 are orthogonal.
88 When the -entropy flag is given an entropy estimate will be computed
90 based on the Quasiharmonic approach and based on Schlitter's formula.
91
93 Options to specify input files:
94 -v [<.trr/.cpt/...>] (eigenvec.trr)
96 Full precision trajectory: trr cpt tng
97 -v2 [<.trr/.cpt/...>] (eigenvec2.trr) (Optional)
99 Full precision trajectory: trr cpt tng
100 -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
102 Trajectory: xtc trr cpt gro g96 pdb tng
103 -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
105 Structure+mass(db): tpr gro g96 pdb brk ent
106 -n [<.ndx>] (index.ndx) (Optional)
108 Index file
109 -eig [<.xvg>] (eigenval.xvg) (Optional)
111 xvgr/xmgr file
112 -eig2 [<.xvg>] (eigenval2.xvg) (Optional)
114 xvgr/xmgr file
115 Options to specify output files:
117 -comp [<.xvg>] (eigcomp.xvg) (Optional)
119 xvgr/xmgr file
120 -rmsf [<.xvg>] (eigrmsf.xvg) (Optional)
122 xvgr/xmgr file
123 -proj [<.xvg>] (proj.xvg) (Optional)
125 xvgr/xmgr file
126 -2d [<.xvg>] (2dproj.xvg) (Optional)
128 xvgr/xmgr file
129 -3d [<.gro/.g96/...>] (3dproj.pdb) (Optional)
131 Structure file: gro g96 pdb brk ent esp
132 -filt [<.xtc/.trr/...>] (filtered.xtc) (Optional)
134 Trajectory: xtc trr cpt gro g96 pdb tng
135 -extr [<.xtc/.trr/...>] (extreme.pdb) (Optional)
137 Trajectory: xtc trr cpt gro g96 pdb tng
138 -over [<.xvg>] (overlap.xvg) (Optional)
140 xvgr/xmgr file
141 -inpr [<.xpm>] (inprod.xpm) (Optional)
143 X PixMap compatible matrix file
144 Other options:
146 -b <time> (0)
148 Time of first frame to read from trajectory (default unit ps)
149 -e <time> (0)
151 Time of last frame to read from trajectory (default unit ps)
152 -dt <time> (0)
154 Only use frame when t MOD dt = first time (default unit ps)
155 -tu <enum> (ps)
157 Unit for time values: fs, ps, ns, us, ms, s
158 -[no]w (no)
160 View output .xvg, .xpm, .eps and .pdb files
161 -xvg <enum> (xmgrace)
163 xvg plot formatting: xmgrace, xmgr, none
164 -first <int> (1)
166 First eigenvector for analysis (-1 is select)
167 -last <int> (-1)
169 Last eigenvector for analysis (-1 is till the last)
170 -skip <int> (1)
172 Only analyse every nr-th frame
173 -max <real> (0)
175 Maximum for projection of the eigenvector on the average struc‐
176 ture, max=0 gives the extremes
177 -nframes <int> (2)
179 Number of frames for the extremes output
180 -[no]split (no)
182 Split eigenvector projections where time is zero
183 -[no]entropy (no)
185 Compute entropy according to the Quasiharmonic formula or
186 Schlitter's method.
187 -temp <real> (298.15)
189 Temperature for entropy calculations
190 -nevskip <int> (6)
192 Number of eigenvalues to skip when computing the entropy due to
193 the quasi harmonic approximation. When you do a rotational
194 and/or translational fit prior to the covariance analysis, you
195 get 3 or 6 eigenvalues that are very close to zero, and which
196 should not be taken into account when computing the entropy.
197
199 gmx(1)
200 More information about GROMACS is available at <‐
202 http://www.gromacs.org/>.
203
205 2022, GROMACS development team
2062022.3 Sep 02, 2022 GMX-ANAEIG(1)