g_nmeig (1) - Linux Manuals

g_nmeig: diagonalizes the Hessian

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