g_nmens(1)
NAME
g_nmens - generates an ensemble of structures from the normal modes
SYNOPSIS
g_nmens -v eigenvec.trr -e eigenval.xvg -s topol.tpr -n index.ndx -o ensemble.xtc -[no]h -nice int -[no]xvgr -temp real -seed int -num int -first int -last int
DESCRIPTION
g_nmens generates an ensemble around an average structure in a subspace
which 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.
FILES
- -v eigenvec.trr Input
- Full precision trajectory: trr trj
- -e eigenval.xvg Input
- xvgr/xmgr file
- -s topol.tpr Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
- -n index.ndx Input, Opt.
- Index file
- -o ensemble.xtc Output
- Generic trajectory: xtc trr trj gro g96 pdb
OTHER OPTIONS
- -[no]h no
- Print help info and quit
- -nice int 19
- Set the nicelevel
- -[no]xvgr yes
- Add specific codes (legends etc.) in the output xvg files for the
- xmgrace program
- -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
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.