Provided by: gromacs-data_2019.3-2_all bug

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, 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 random 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 and -v2 are given, a single number for the overlap between the covariance 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

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

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

       -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

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

       -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 Schlitter’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 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.

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2019, GROMACS development team