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- jessie 5.0.2-1
gmx-nmens(1) | GROMACS Manual | gmx-nmens(1) |
NAME¶
gmx-nmens - Generate an ensemble of structures from the normal modesSYNOPSIS¶
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>]
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)
SEE ALSO¶
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.VERSION 5.0.2 |