gmx-nmens man page

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


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>]


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 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


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

Referenced By


Explore man page connections for gmx-nmens(1).

GROMACS Aug 04, 2016