Normal-Mode Analysis#
Normal-mode analysis 5456
can be performed using GROMACS, by diagonalization of the
mass-weighted Hessian
where
First the Hessian matrix, which is a
where
where
A number of GROMACS programs are involved in these calculations. First, the energy should be minimized using mdrun. Then, mdrun computes the Hessian. Note that for generating the run input file, one should use the minimized conformation from the full precision trajectory file, as the structure file is not accurate enough. gmx nmeig does the diagonalization and the sorting of the normal modes according to their frequencies. Both mdrun and gmx nmeig should be run in double precision. The normal modes can be analyzed with the program gmx anaeig. Ensembles of structures at any temperature and for any subset of normal modes can be generated with gmx nmens. An overview of normal-mode analysis and the related principal component analysis (see sec. Covariance analysis) can be found in 57.