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g_nmeig - diagonalizes the HessianVERSION4.0.1

g_nmeig-fhessian.mtx-stopol.tpr-ofeigenfreq.xvg-oleigenval.xvg-veigenvec.trr-[no]h-niceint-[no]xvgr-[no]m-firstint-lastint

g_nmeig calculates the eigenvectors/values of a (Hessian) matrix, which can be calculated withmdrun. 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 withg_anaeig. An ensemble of structures can be generated from the eigenvectors withg_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).

-fhessian.mtxInputHessian matrix-stopol.tprInputStructure+mass(db): tpr tpb tpa gro g96 pdb-ofeigenfreq.xvgOutputxvgr/xmgr file-oleigenval.xvgOutputxvgr/xmgr file-veigenvec.trrOutputFull precision trajectory: trr trj cpt

-[no]hnoPrint help info and quit-niceint19Set the nicelevel-[no]xvgryesAdd specific codes (legends etc.) in the output xvg files for the xmgrace program-[no]myesDivide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for â€™Normal Modesâ€™ analysis-firstint1First eigenvector to write away-lastint50Last eigenvector to write away

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Thu 16 Oct 2008 g_nmeig(1)