home | help 
GMX-ANAEIG(1)			     GROMACS			   GMX-ANAEIG(1)

NAME
     gmx-anaeig - Analyze eigenvectors/normal modes

SYNOPSIS
	gmx anaeig [-v [<.trr/.cpt/...>]] [-v2 [<.trr/.cpt/...>]]
		   [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
		   [-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>]] [-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 covariance
     matrix (gmx covar) or of a Normal Modes analysis (gmx nmeig).

     When a trajectory is projected on eigenvectors, all structures  are  fitted
     to  the  structure  in  the  eigenvector file, if present, otherwise to the
     structure in the structure file. When no run input file is supplied,  peri-
     odicity  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 covari-
     ance 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 random diffusion
     are cosines with the number of periods equal to half the pc index.  The co-
     sine 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 av-
     erage 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  -nmr-
     pdb 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 and -v2 are given, a single number for the overlap between the  co-
     variance  matrices  is  generated. Note that the eigenvalues are by default
     read from the timestamp field in the  eigenvector	input  files,  but  when
     -eig,  or	-eig2 are given, the corresponding eigenvalues are used instead.
     The formulas are:

		difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2))
	normalized overlap = 1 - difference/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 files:

     -v [<.trr/.cpt/...>] (eigenvec.trr)
	    Full precision trajectory: trr cpt tng h5md

     -v2 [<.trr/.cpt/...>] (eigenvec2.trr) (Optional)
	    Full precision trajectory: trr cpt tng h5md

     -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
	    Trajectory: xtc trr cpt gro g96 pdb tng h5md

     -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
	    Structure+mass(db): tpr gro g96 pdb brk ent

     -n [<.ndx>] (index.ndx) (Optional)
	    Index file

     -eig [<.xvg>] (eigenval.xvg) (Optional)
	    xvgr/xmgr file

     -eig2 [<.xvg>] (eigenval2.xvg) (Optional)
	    xvgr/xmgr file

     Options to specify output files:

     -comp [<.xvg>] (eigcomp.xvg) (Optional)
	    xvgr/xmgr file

     -rmsf [<.xvg>] (eigrmsf.xvg) (Optional)
	    xvgr/xmgr file

     -proj [<.xvg>] (proj.xvg) (Optional)
	    xvgr/xmgr file

     -2d [<.xvg>] (2dproj.xvg) (Optional)
	    xvgr/xmgr file

     -3d [<.gro/.g96/...>] (3dproj.pdb) (Optional)
	    Structure file: gro g96 pdb brk ent esp

     -filt [<.xtc/.trr/...>] (filtered.xtc) (Optional)
	    Trajectory: xtc trr cpt gro g96 pdb tng h5md

     -extr [<.xtc/.trr/...>] (extreme.pdb) (Optional)
	    Trajectory: xtc trr cpt gro g96 pdb tng h5md

     -over [<.xvg>] (overlap.xvg) (Optional)
	    xvgr/xmgr file

     -inpr [<.xpm>] (inprod.xpm) (Optional)
	    X PixMap compatible matrix file

     Other options:

     -b <time> (0)
	    Time of first frame to read from trajectory (default unit ps)

     -e <time> (0)
	    Time of last frame to read from trajectory (default unit ps)

     -dt <time> (0)
	    Only use frame when t MOD dt = first time (default unit ps)

     -tu <enum> (ps)
	    Unit for time values: 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 trans-
	    lational fit prior to the covariance analysis, you get 3 or 6 eigen-
	    values that are very close to zero, and which should  not  be  taken
	    into account when computing the entropy.

SEE ALSO
     gmx(1)

     More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT
     2026, GROMACS development team

2026.3				  Jun 25, 2026			   GMX-ANAEIG(1)
home | help