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)