g_nmens1
Generate an ensemble of structures from the normal modes
Part of gmx-nmens(1).
Usage
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>]
Overview
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)
Releases
5 releases since Debian 4.0 (Etch); the text changed 4 times.