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"But since the DFT works not so well when dealing with semiconductors and excited-state calculations, wouldn't NAMD be too erroneous considering the nuclei vibrations?" First of all, DFT in this context might not be as bad as you think. For example, my answer to: What are some recent developments in density functional theory? shows that even 10 ...


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You may find derivation of eqs.120-124 in these notes Normal modes. The true story. helpful in revising your derivation. Answering the other question: centre-of-mass can always be separated by the choice of centre-of-mass coordinates (cf. eq. 109-118) in Normal modes. The true story.. In almost all nuclear motion calculations the mass-polarisation term ...


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