Main Table of Contents

Fri 5 Jul 2013


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.


-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]h bool no Print help info and quit
-[no]version bool no 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)