.. _gmx nmens: gmx nmens ========= Synopsis -------- .. parsed-literal:: gmx nmens [:strong:`-v` :emphasis:`[<.trr/.cpt/...>]`] [:strong:`-e` :emphasis:`[<.xvg>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-o` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-xvg` :emphasis:``] [:strong:`-temp` :emphasis:``] [:strong:`-seed` :emphasis:``] [:strong:`-num` :emphasis:``] [:strong:`-first` :emphasis:``] [:strong:`-last` :emphasis:``] 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: :ref:`trr` :ref:`cpt` :ref:`tng` ``-e`` [<.xvg>] (eigenval.xvg) xvgr/xmgr file ``-s`` [<.tpr/.gro/...>] (topol.tpr) Structure+mass(db): :ref:`tpr` :ref:`gro` :ref:`g96` :ref:`pdb` brk ent ``-n`` [<.ndx>] (index.ndx) (Optional) Index file Options to specify output files: ``-o`` [<.xtc/.trr/...>] (ensemble.xtc) Trajectory: :ref:`xtc` :ref:`trr` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng` Other options: ``-xvg`` (xmgrace) xvg plot formatting: xmgrace, xmgr, none ``-temp`` (300) Temperature in Kelvin ``-seed`` (0) Random seed (0 means generate) ``-num`` (100) Number of structures to generate ``-first`` (7) First eigenvector to use (-1 is select) ``-last`` (-1) Last eigenvector to use (-1 is till the last) .. only:: man See also -------- :manpage:`gmx(1)` More information about |Gromacs| is available at .