Main Table of Contents

Thu 26 Aug 2010


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).


-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]h gmx_bool no Print help info and quit
-[no]version gmx_bool no Print version info and quit
-nice int 19 Set the nicelevel
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]m gmx_bool 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