Synopsis
gmx nmens [-v [<.trr/.cpt/...>]] [-e [<.xvg>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-nice ] [-xvg ]
[-temp ] [-seed ] [-num ] [-first ]
[-last ]
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 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)
