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GMX-NMENS(1) GROMACS 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/.gro/...>]] [-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-xvg <enum>] [-temp <real>] [-seed <int>] [-num <int>] [-first <int>] [-last <int>] DESCRIPTION gmx nmens generates an ensemble around an average structure in a sub- space 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 vari- ance 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: 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 gmx(1) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-NMENS(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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