gmx-anaeig(1) GROMACS Manual gmx-anaeig(1)NAMEgmx-anaeig - Analyze eigenvectors/normal modes
SYNOPSIS
gmx anaeig [-v [<.trr/.cpt/...>]] [-v2 [<.trr/.cpt/...>]]
[-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-eig [<.xvg>]] [-eig2 [<.xvg>]]
[-comp [<.xvg>]] [-rmsf [<.xvg>]] [-proj [<.xvg>]]
[-2d [<.xvg>]] [-3d [<.gro/.g96/...>]]
[-filt [<.xtc/.trr/...>]] [-extr [<.xtc/.trr/...>]]
[-over [<.xvg>]] [-inpr [<.xpm>]] [-nice <int>]
[-b <time>] [-e <time>] [-dt <time>] [-tu <enum>] [-[no]w]
[-xvg <enum>] [-first <int>] [-last <int>] [-skip <int>]
[-max <real>] [-nframes <int>] [-[no]split] [-[no]entropy]
[-temp <real>] [-nevskip <int>]
DESCRIPTION
gmx anaeig analyzes eigenvectors. The eigenvectors can be of a covari‐
ance matrix (gmx covar) or of a Normal Modes analysis (gmx nmeig).
When a trajectory is projected on eigenvectors, all structures are fit‐
ted to the structure in the eigenvector file, if present, otherwise to
the structure in the structure file. When no run input file is sup‐
plied, periodicity will not be taken into account. Most analyses are
performed on eigenvectors -first to -last, but when -first is set to -1
you will be prompted for a selection.
-comp: plot the vector components per atom of eigenvectors -first to
-last.
-rmsf: plot the RMS fluctuation per atom of eigenvectors -first to
-last (requires -eig).
-proj: calculate projections of a trajectory on eigenvectors -first to
-last. The projections of a trajectory on the eigenvectors of its
covariance matrix are called principal components (pc's). It is often
useful to check the cosine content of the pc's, since the pc's of ran‐
dom diffusion are cosines with the number of periods equal to half the
pc index. The cosine content of the pc's can be calculated with the
program gmx analyze.
-2d: calculate a 2d projection of a trajectory on eigenvectors -first
and -last.
-3d: calculate a 3d projection of a trajectory on the first three
selected eigenvectors.
-filt: filter the trajectory to show only the motion along eigenvectors
-first to -last.
-extr: calculate the two extreme projections along a trajectory on the
average structure and interpolate -nframes frames between them, or set
your own extremes with -max. The eigenvector -first will be written
unless -first and -last have been set explicitly, in which case all
eigenvectors will be written to separate files. Chain identifiers will
be added when writing a .pdb file with two or three structures (you can
use rasmol -nmrpdb to view such a .pdb file).
Overlap calculations between covariance analysis: Note: the analysis
should use the same fitting structure
-over: calculate the subspace overlap of the eigenvectors in file -v2
with eigenvectors -first to -last in file -v.
-inpr: calculate a matrix of inner-products between eigenvectors in
files -v and -v2. All eigenvectors of both files will be used unless
-first and -last have been set explicitly.
When -v, -eig, -v2 and -eig2 are given, a single number for the overlap
between the covariance matrices is generated. The formulas are: differ‐
ence = sqrt(tr((sqrt(M1) - sqrt(M2))2)) normalized overlap = 1 - dif‐
ference/sqrt(tr(M1) + tr(M2)) shape overlap = 1 -
sqrt(tr((sqrt(M1/tr(M1)) - sqrt(M2/tr(M2)))2)) where M1 and M2 are the
two covariance matrices and tr is the trace of a matrix. The numbers
are proportional to the overlap of the square root of the fluctuations.
The normalized overlap is the most useful number, it is 1 for identical
matrices and 0 when the sampled subspaces are orthogonal.
When the -entropy flag is given an entropy estimate will be computed
based on the Quasiharmonic approach and based on Schlitter's formula.
OPTIONS
Options to specify input and output files:
-v [<.trr/.cpt/...>] (eigenvec.trr) (Input)
Full precision trajectory: trr cpt trj tng
-v2 [<.trr/.cpt/...>] (eigenvec2.trr) (Input, Optional)
Full precision trajectory: trr cpt trj tng
-f [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-eig [<.xvg>] (eigenval.xvg) (Input, Optional)
xvgr/xmgr file
-eig2 [<.xvg>] (eigenval2.xvg) (Input, Optional)
xvgr/xmgr file
-comp [<.xvg>] (eigcomp.xvg) (Output, Optional)
xvgr/xmgr file
-rmsf [<.xvg>] (eigrmsf.xvg) (Output, Optional)
xvgr/xmgr file
-proj [<.xvg>] (proj.xvg) (Output, Optional)
xvgr/xmgr file
-2d [<.xvg>] (2dproj.xvg) (Output, Optional)
xvgr/xmgr file
-3d [<.gro/.g96/...>] (3dproj.pdb) (Output, Optional)
Structure file: gro g96 pdb brk ent esp
-filt [<.xtc/.trr/...>] (filtered.xtc) (Output, Optional)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-extr [<.xtc/.trr/...>] (extreme.pdb) (Output, Optional)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-over [<.xvg>] (overlap.xvg) (Output, Optional)
xvgr/xmgr file
-inpr [<.xpm>] (inprod.xpm) (Output, Optional)
X PixMap compatible matrix file
Other options:
-nice <int> (19)
Set the nicelevel
-b <time> (0)
First frame (ps) to read from trajectory
-e <time> (0)
Last frame (ps) to read from trajectory
-dt <time> (0)
Only use frame when t MOD dt = first time (ps)
-tu <enum> (ps)
Time unit: fs, ps, ns, us, ms, s
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-first <int> (1)
First eigenvector for analysis (-1 is select)
-last <int> (-1)
Last eigenvector for analysis (-1 is till the last)
-skip <int> (1)
Only analyse every nr-th frame
-max <real> (0)
Maximum for projection of the eigenvector on the average structure,
max=0 gives the extremes
-nframes <int> (2)
Number of frames for the extremes output
-[no]split (no)
Split eigenvector projections where time is zero
-[no]entropy (no)
Compute entropy according to the Quasiharmonic formula or Schlit‐
ter's method.
-temp <real> (298.15)
Temperature for entropy calculations
-nevskip <int> (6)
Number of eigenvalues to skip when computing the entropy due to the
quasi harmonic approximation. When you do a rotational and/or transla‐
tional 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.
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-anaeig(1)
