NAME

       gmx-nmens - Generate an ensemble of structures from the normal modes

SYNOPSIS

          gmx nmens [-v [<.trr/.cpt/...>]] [-e [<.xvg>]] [-s [<.tpr/.gro/...>]]
                    [-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-xvg <enum>]
                    [-temp <real>] [-seed <int>] [-num <int>] [-first <int>]
                    [-last <int>]

DESCRIPTION

       gmx  nmens generates an ensemble around an average structure in a subspace that is defined
       by  a  set  of  normal  modes  (eigenvectors).   The  eigenvectors  are  assumed   to   be
       mass-weighted.   The  position  along  each  eigenvector is randomly taken from a Gaussian
       distribution with variance kT/eigenvalue.

       By default the starting eigenvector is set to 7, since the first six normal modes are  the
       translational and rotational degrees of freedom.

OPTIONS

       Options to specify input files:

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

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

       -s [<.tpr/.gro/...>] (topol.tpr)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -o [<.xtc/.trr/...>] (ensemble.xtc)
              Trajectory: xtc trr gro g96 pdb tng

       Other options:

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

       -temp <real> (300)
              Temperature in Kelvin

       -seed <int> (0)
              Random seed (0 means generate)

       -num <int> (100)
              Number of structures to generate

       -first <int> (7)
              First eigenvector to use (-1 is select)

       -last <int> (-1)
              Last eigenvector to use (-1 is till the last)

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2024, GROMACS development team