table of contents
g_nmens(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_nmens(1) |
NAME¶
g_nmens - generates an ensemble of structures from the normal modesSYNOPSIS¶
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 intDESCRIPTION¶
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.FILES¶
-v eigenvec.trr InputFull precision trajectory: trr trj cpt
xvgr/xmgr file
Structure+mass(db): tpr tpb tpa gro g96 pdb
Index file
Trajectory: xtc trr trj gro g96 pdb
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
xvg plot formatting: xmgrace, xmgr or none
Temperature in Kelvin
Random seed, -1 generates a seed from time and pid
Number of structures to generate
First eigenvector to use (-1 is select)
Last eigenvector to use (-1 is till the last)
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |