NAME

       g_nmeig - diagonalizes the Hessian VERSION 4.6.5

SYNOPSIS

       g_nmeig   -f   hessian.mtx   -s  topol.tpr  -of  eigenfreq.xvg  -ol  eigenval.xvg  -os  spectrum.xvg  -qc
       quant_corr.xvg -v eigenvec.trr -[no]h -[no]version -nice int  -xvg  enum  -[no]m  -first  int  -last  int
       -maxspec int -T real -[no]constr -width real

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.

       This  program  can  be  optionally  used  to compute quantum corrections to heat capacity and enthalpy by
       providing an extra file argument  -qcorr. See the GROMACS manual, Chapter  1,  for  details.  The  result
       includes  subtracting  a  harmonic  degree  of freedom at the given temperature.  The total correction is
       printed on the terminal screen.  The recommended way of getting the corrections out is:

        g_nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-constr]

       The  -constr option should be used when bond constraints were used during the  simulation   for  all  the
       covalent bonds. If this is not the case, you need to analyze the  quant_corr.xvg file yourself.

       To make things more flexible, the program can also take virtual sites into account when computing quantum
       corrections. When selecting  -constr and  -qc, the  -begin and  -end options will be set automatically as
       well.  Again, if you think you know it better, please check the  eigenfreq.xvg output.

FILES

       -f hessian.mtx Input
        Hessian matrix

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -of eigenfreq.xvg Output
        xvgr/xmgr file

       -ol eigenval.xvg Output
        xvgr/xmgr file

       -os spectrum.xvg Output, Opt.
        xvgr/xmgr file

       -qc quant_corr.xvg Output, Opt.
        xvgr/xmgr file

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

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 19
        Set the nicelevel

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -[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

       -maxspec int 4000
        Highest frequency (1/cm) to consider in the spectrum

       -T real 298.15
        Temperature for computing quantum heat capacity and enthalpy when  using  normal  mode  calculations  to
       correct classical simulations

       -[no]constrno
        If  constraints were used in the simulation but not in the normal mode analysis (this is the recommended
       way of doing it) you will need to set this for computing the quantum corrections.

       -width real 1
        Width (sigma) of the gaussian peaks (1/cm) when generating a spectrum

SEE ALSO

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                       g_nmeig(1)