debian man page for g_nmens

g_nmens(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					g_nmens(1)

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/>.

								  Mon 4 Apr 2011							g_nmens(1)