DragonFly On-Line Manual Pages

gmx-nmens(1)                    GROMACS Manual                    gmx-nmens(1)

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

SYNOPSIS
       gmx nmens [-v [<.trr/.cpt/...>]] [-e [<.xvg>]]
                 [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]] [-o [<.xtc/.trr/...>]]
                 [-nice <int>] [-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 and output files:

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

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

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

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

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

       Other options:

       -nice <int> (19)
           Set the nicelevel

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

       -temp <real> (300)
           Temperature in Kelvin

       -seed <int> (-1)
           Random seed, -1 generates a seed from time and pid

       -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
       gromacs(7)

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

VERSION 5.0.6                                                     gmx-nmens(1)