g_nmeig(1)
NAME
g_nmeig - diagonalizes the Hessian
SYNOPSIS
g_nmeig -f hessian.mtx -s topol.tpr -of eigenfreq.xvg -ol eigenval.xvg -v eigenvec.trr -[no]h -nice int -[no]xvgr -[no]m -first int -last int
DESCRIPTION
g_nmeig calculates the eigenvectors/values of a (Hessian) matrix, which
can be calculated with mdrun The eigenvectors are written to a trajectory file ( -v ). The structure is written first with t=0. The eigenvectors are written as frames with the eigenvector number as timestamp.
The eigenvectors can be analyzed with g_anaeig An ensemble of structures can be generated from the eigenvectors with
g_nmens . When mass weighting is used, the generated eigenvectors will be scaled back to plain cartesian coordinates before generating the output - in this case they will no longer be exactly orthogonal in the standard cartesian norm (But in the mass weighted norm they would be).
FILES
- -f hessian.mtx Input
- Hessian matrix
- -s topol.tpr Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
- -of eigenfreq.xvg Output
- xvgr/xmgr file
- -ol eigenval.xvg Output
- xvgr/xmgr file
- -v eigenvec.trr Output
- Full precision trajectory: trr trj
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
- -[no]m yes
- Divide elements of Hessian by product of sqrt(mass) of involved atoms
- prior to diagonalization. This should be used for 'Normal Modes' analysis
- -first int 1
- First eigenvector to write away
- -last int 50
- Last eigenvector to write away
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.