Provided by: gromacs-data_4.6.5-1build1_all bug


       g_nmeig - diagonalizes the Hessian VERSION 4.6.5


       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


        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.


       -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


        Print help info and quit

        Print version info and quit

       -nice int 19
        Set the nicelevel

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

        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

        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

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



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                               g_nmeig(1)