gmx nmeig [-f [<.mtx>]] [-s [<.tpr>]] [-of [<.xvg>]] [-ol [<.xvg>]]
[-os [<.xvg>]] [-qc [<.xvg>]] [-v [<.trr/.cpt/...>]]
[-xvg <enum>] [-[no]m] [-first <int>] [-last <int>]
[-maxspec <int>] [-T <real>] [-[no]constr] [-width <real>]
gmx nmeig calculates the eigenvectors/values of a (Hessian) matrix, which can be calculated with gmx 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 gmx anaeig. An ensemble of structures can be generated from the eigenvectors with gmx 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:
gmx 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.
Options to specify input files:
Options to specify output files:
Other options: