gmx-nmens1
Generate an ensemble of structures from the normal modes
Usage
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>]
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 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) |
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.