NAME
g_nmens - generates an ensemble of structures from the normal modes
VERSION 4.0.1
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 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
-nice int 19
Set the nicelevel
-[no]xvgryes
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
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_nmens(1)