Provided by: gromacs-data_4.6.5-1build1_all

**NAME**

g_nmeig - diagonalizes the HessianVERSION4.6.5

**SYNOPSIS**

g_nmeig-fhessian.mtx-stopol.tpr-ofeigenfreq.xvg-oleigenval.xvg-osspectrum.xvg-qcquant_corr.xvg-veigenvec.trr-[no]h-[no]version-niceint-xvgenum-[no]m-firstint-lastint-maxspecint-Treal-[no]constr-widthreal

**DESCRIPTION**

g_nmeigcalculates 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. This program can be optionally used to compute quantum corrections to heat capacity and enthalpy by providing an extra file argument-qcorr. See the GROMACS manual, Chapter 1, for details. The result includes subtracting a harmonic degree of freedom at the given temperature. The total correction is printed on the terminal screen. The recommended way of getting the corrections out is:g_nmeig-stopol.tpr-fnm.mtx-first7-last10000-T300-qc[-constr]The-constroption should be used when bond constraints were used during the simulationforallthecovalentbonds. If this is not the case, you need to analyze thequant_corr.xvgfile yourself. To make things more flexible, the program can also take virtual sites into account when computing quantum corrections. When selecting-constrand-qc, the-beginand-endoptions will be set automatically as well. Again, if you think you know it better, please check theeigenfreq.xvgoutput.

**FILES**

-fhessian.mtxInputHessian matrix-stopol.tprInputRun input file: tpr tpb tpa-ofeigenfreq.xvgOutputxvgr/xmgr file-oleigenval.xvgOutputxvgr/xmgr file-osspectrum.xvgOutput,Opt.xvgr/xmgr file-qcquant_corr.xvgOutput,Opt.xvgr/xmgr file-veigenvec.trrOutputFull precision trajectory: trr trj cpt

**OTHER** **OPTIONS**

-[no]hnoPrint help info and quit-[no]versionnoPrint version info and quit-niceint19Set the nicelevel-xvgenumxmgracexvg plot formatting:xmgrace,xmgrornone-[no]myesDivide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis-firstint1First eigenvector to write away-lastint50Last eigenvector to write away-maxspecint4000Highest frequency (1/cm) to consider in the spectrum-Treal298.15Temperature for computing quantum heat capacity and enthalpy when using normal mode calculations to correct classical simulations-[no]constrnoIf constraints were used in the simulation but not in the normal mode analysis (this is the recommended way of doing it) you will need to set this for computing the quantum corrections.-widthreal1Width (sigma) of the gaussian peaks (1/cm) when generating a spectrum

**SEE** **ALSO**

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Mon 2 Dec 2013 g_nmeig(1)