1GMX-NMENS(1)                        GROMACS                       GMX-NMENS(1)
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NAME

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

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

15       gmx  nmens  generates an ensemble around an average structure in a sub‐
16       space that is defined by a set of  normal  modes  (eigenvectors).   The
17       eigenvectors  are assumed to be mass-weighted.  The position along each
18       eigenvector is randomly taken from a Gaussian distribution  with  vari‐
19       ance kT/eigenvalue.
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21       By  default  the  starting eigenvector is set to 7, since the first six
22       normal modes are the translational and rotational degrees of freedom.
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OPTIONS

25       Options to specify input files:
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27       -v [<.trr/.cpt/…>] (eigenvec.trr)
28              Full precision trajectory: trr cpt tng
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30       -e [<.xvg>] (eigenval.xvg)
31              xvgr/xmgr file
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33       -s [<.tpr/.gro/…>] (topol.tpr)
34              Structure+mass(db): tpr gro g96 pdb brk ent
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36       -n [<.ndx>] (index.ndx) (Optional)
37              Index file
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39       Options to specify output files:
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41       -o [<.xtc/.trr/…>] (ensemble.xtc)
42              Trajectory: xtc trr gro g96 pdb tng
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44       Other options:
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46       -xvg <enum> (xmgrace)
47              xvg plot formatting: xmgrace, xmgr, none
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49       -temp <real> (300)
50              Temperature in Kelvin
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52       -seed <int> (0)
53              Random seed (0 means generate)
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55       -num <int> (100)
56              Number of structures to generate
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58       -first <int> (7)
59              First eigenvector to use (-1 is select)
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61       -last <int> (-1)
62              Last eigenvector to use (-1 is till the last)
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SEE ALSO

65       gmx(1)
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67       More    information    about    GROMACS    is    available    at     <‐
68       http://www.gromacs.org/>.
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71       2019, GROMACS development team
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762019.2                           Apr 16, 2019                     GMX-NMENS(1)
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