NAME¶

g_nmens - generates an ensemble of structures from the normal modes VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS¶

g_nmens -v eigenvec.trr -e eigenval.xvg -s topol.tpr -n index.ndx -o ensemble.xtc -[no]h -[no]version -nice int -xvg enum -temp real -seed int -num int -first int -last int

DESCRIPTION¶

g_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.

FILES¶

-v eigenvec.trr Input
Full precision trajectory: trr trj cpt -e eigenval.xvg Input
xvgr/xmgr file -s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt.
Index file -o ensemble.xtc Output
Trajectory: xtc trr trj gro g96 pdb

OTHER OPTIONS¶

-[no]hno
Print help info and quit -[no]versionno
Print version info and quit -nice int 19
Set the nicelevel -xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or 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/>.