NAME¶

g_nmeig - diagonalizes the Hessian VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS¶

g_nmeig -f hessian.mtx -s topol.tpr -of eigenfreq.xvg -ol eigenval.xvg -qc quant_corr.xvg -v eigenvec.trr -[no]h -[no]version -nice int -xvg enum -[no]m -first int -last int -T real -[no]constr

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. 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 -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-constr] The -constr option should be used when bond constraints were used during the simulation for all the covalent bonds. If this is not the case, you need to analyze the quant_corr.xvg file yourself. To make things more flexible, the program can also take virtual sites into account when computing quantum corrections. When selecting -constr and -qc, the -begin and -end options will be set automatically as well. Again, if you think you know it better, please check the eigenfreq.xvg output.

FILES¶

-f hessian.mtx Input
Hessian matrix -s topol.tpr Input
Run input file: tpr tpb tpa -of eigenfreq.xvg Output
xvgr/xmgr file -ol eigenval.xvg Output
xvgr/xmgr file -qc quant_corr.xvg Output, Opt.
xvgr/xmgr file -v eigenvec.trr Output
Full precision trajectory: trr trj cpt

OTHER OPTIONS¶

-[no]hno
Print help info and quit -[no]versionno
Print version info and quit -nice int 19
Set the nicelevel -xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none -[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 -T real 298.15
Temperature for computing quantum heat capacity and enthalpy when using normal mode calculations to correct classical simulations -[no]constrno
If 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.

SEE ALSO¶

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.