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g_nmens_d

NAME

g_nmens - generates an ensemble of structures from the normal modes

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)

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.