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gmx-nmeig(1)                    GROMACS Manual                    gmx-nmeig(1)

NAME
       gmx-nmeig - Diagonalize the Hessian for normal mode analysis

SYNOPSIS
       gmx nmeig [-f [<.mtx>]] [-s [<.tpr/.tpb/...>]] [-of [<.xvg>]]
                 [-ol [<.xvg>]] [-os [<.xvg>]] [-qc [<.xvg>]]
                 [-v [<.trr/.cpt/...>]] [-nice <int>] [-xvg <enum>] [-[no]m]
                 [-first <int>] [-last <int>] [-maxspec <int>] [-T <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 as
       timestamp. 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.
       Again, if you think you know it better, please check the eigenfreq.xvg
       output.

OPTIONS
       Options to specify input and output files:

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

       -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
           Run input file: tpr tpb tpa

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

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

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

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

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

       Other options:

       -nice <int> (19)
           Set the nicelevel

       -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

       -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]constr  (no)
           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/>.

VERSION 5.0.6                                                     gmx-nmeig(1)