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g_nmens

Langue: en

Autres versions - même langue

Version: 370436 (fedora - 01/12/10)

Section: 1 (Commandes utilisateur)

Sommaire

NAME

g_nmens - generates an ensemble of structures from the normal modes

VERSION 4.5

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 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

-[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)