man g_nmeig (Commandes) - g_nmeig VERSION 3.3_beta_20050823
NAME
g_nmeig VERSION 3.3_beta_20050823
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 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