NAME

       gmx-nmeig - Diagonalize the Hessian for normal mode analysis

SYNOPSIS

          gmx nmeig [-f [<.mtx>]] [-s [<.tpr>]] [-of [<.xvg>]] [-ol [<.xvg>]]
                    [-os [<.xvg>]] [-qc [<.xvg>]] [-v [<.trr/.cpt/...>]]
                    [-xvg <enum>] [-[no]m] [-first <int>] [-last <int>]
                    [-maxspec <int>] [-T <real>] [-P <real>] [-sigma <int>]
                    [-scale <real>] [-linear_toler <real>] [-[no]constr]
                    [-width <real>]

DESCRIPTION

       gmx  nmeig  calculates  the  eigenvectors/values  of a (Hessian) matrix, which can be calculated with gmx
       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 and eigenvalue written as step number
       and timestamp, respectively.  The  eigenvectors  can  be  analyzed  with  gmx  anaeig.   An  ensemble  of
       structures  can  be  generated  from  the  eigenvectors  with gmx 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:

       gmx 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.

       Based on a harmonic analysis of the normal  mode  frequencies,  thermochemical  properties  S0  (Standard
       Entropy),  Cv (Heat capacity at constant volume), Zero-point energy and the internal energy are computed,
       much in the same manner as popular quantum chemistry programs.

OPTIONS

       Options to specify input files:

       -f [<.mtx>] (hessian.mtx)
              Hessian matrix

       -s [<.tpr>] (topol.tpr)
              Portable xdr run input file

       Options to specify output files:

       -of [<.xvg>] (eigenfreq.xvg)
              xvgr/xmgr file

       -ol [<.xvg>] (eigenval.xvg)
              xvgr/xmgr file

       -os [<.xvg>] (spectrum.xvg) (Optional)
              xvgr/xmgr file

       -qc [<.xvg>] (quant_corr.xvg) (Optional)
              xvgr/xmgr file

       -v [<.trr/.cpt/...>] (eigenvec.trr)
              Full precision trajectory: trr cpt tng

       Other options:

       -xvg <enum> (xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -[no]m (yes)
              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. -1 is use all dimensions.

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

       -T <real> (298.15)
              Temperature  for  computing  entropy,  quantum  heat  capacity and enthalpy when using normal mode
              calculations to correct classical simulations

       -P <real> (1)
              Pressure (bar) when computing entropy

       -sigma <int> (1)
              Number of symmetric copies used when computing entropy. E.g. for water the number is 2, for NH3 it
              is 3 and for methane it is 12.

       -scale <real> (1)
              Factor to scale frequencies before computing thermochemistry values

       -linear_toler <real> (1e-05)
              Tolerance  for  determining  whether  a  compound  is  linear as determined from the ration of the
              moments inertion Ix/Iy and Ix/Iz.

       -[no]constr (no)
              If constraints were used in the simulation but not in the normal mode analysis 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

       gmx(1)

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

COPYRIGHT

       2020, GROMACS development team