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

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                      GMX-NMENS(1)

gmxnmens  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.

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

       Options to specify input files:

       -v[<.trr/.cpt/...>](eigenvec.trr)
              Full precision trajectory: trrcpttng-e[<.xvg>](eigenval.xvg)
              xvgr/xmgr file

       -s[<.tpr/.gro/...>](topol.tpr)
              Structure+mass(db): tprgrog96pdb brk ent

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

       Options to specify output files:

       -o[<.xtc/.trr/...>](ensemble.xtc)
              Trajectory: xtctrrgrog96pdbtng

       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)

gmx(1)

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

          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>]