man g_nmens (Commandes) - g_nmens VERSION 3.3_beta_20050823
NAME
g_nmens VERSION 3.3_beta_20050823
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)