NAME
g_nmeig - diagonalizes the Hessian
VERSION 4.0.1
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
-of eigenfreq.xvg Output
xvgr/xmgr file
-ol eigenval.xvg Output
xvgr/xmgr file
-v eigenvec.trr Output
Full precision trajectory: trr trj cpt
OTHER OPTIONS
-[no]hno
Print help info and quit
-nice int 19
Set the nicelevel
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-[no]myes
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
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_nmeig(1)