Provided by: gromacs-data_2019.1-1_all bug


       gmx-nmeig - Diagonalize the Hessian for normal mode analysis


          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>]


       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


       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



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       2019, GROMACS development team