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 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: 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/>.
COPYRIGHT
2020, GROMACS development team