gmx nmens¶
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:
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)