g_nmens(1) - Linux man page

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 -xvgenum -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)