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NAME

       g_nmeig - diagonalizes the Hessian

       VERSION 4.0.1

SYNOPSIS

       g_nmeig  -f hessian.mtx -s topol.tpr -of eigenfreq.xvg -ol eigenval.xvg
       -v eigenvec.trr -[no]h -nice int -[no]xvgr -[no]m -first int -last int

DESCRIPTION

       g_nmeig calculates the eigenvectors/values of a (Hessian) matrix, which
       can  be  calculated  with   mdrun.   The  eigenvectors are written to a
       trajectory file ( -v).  The structure is written first  with  t=0.  The
       eigenvectors  are  written  as  frames  with  the eigenvector number as
       timestamp.  The  eigenvectors  can  be  analyzed  with   g_anaeig.   An
       ensemble  of  structures  can  be generated from the eigenvectors with
       g_nmens. When mass weighting is used, the generated  eigenvectors  will
       be  scaled  back  to  plain cartesian coordinates before generating the
       output - in this case they will no longer be exactly orthogonal in  the
       standard  cartesian norm (But in the mass weighted norm they would be).

FILES

       -f hessian.mtx Input
        Hessian matrix

       -s topol.tpr Input
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -of eigenfreq.xvg Output
        xvgr/xmgr file

       -ol eigenval.xvg Output
        xvgr/xmgr file

       -v eigenvec.trr Output
        Full precision trajectory: trr trj cpt

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -nice int 19
        Set the nicelevel

       -[no]xvgryes
        Add specific codes (legends etc.) in the  output  xvg  files  for  the
       xmgrace program

       -[no]myes
        Divide  elements of Hessian by product of sqrt(mass) of involved atoms
       prior to diagonalization.  This  should  be  used  for  ’Normal  Modes’
       analysis

       -first int 1
        First eigenvector to write away

       -last int 50
        Last eigenvector to write away

SEE ALSO

       gromacs(7)

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

                                Thu 16 Oct 2008                     g_nmeig(1)