This is an on-line material of my lectures in molecular science summer school 2021. The lecture is aimed at those who are interested in computational chemistry, and want to develop the skills to perform electronic structure calculations, molecular dynamics (MD) simulations, hybrid quantum mechanics / molecular mechanics (QM/MM) calculations, and anharmonic vibrational calculations.
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Electronic structure calculations using Gaussian16
- 3.1. Basic: Water molecule
- 3.2. ESP surface of imidazole
- 3.3. Excited states of rhodamine
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MD simulations using GENESIS
- 5.1. Basic MD: Protein G
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QM/MM calculations using GENESIS and DFTB+
- 7.1. QM/MM-MD: Phosphate ion in solution
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Vibrational calculations using SINDO
- 9.1. VCI and VQDPT2 with multi-resolution PES: Formaldehyde
- 9.2. VQDPT2 with local modes: Water trimer and hexamer
- 9.3. VQDPT2 with QM/MM potential: Phosphate ion in solution
Kiyoshi Yagi
Theoretical Molecular Science Laboratory,
Clusters for Pioneering Research,
RIKEN
kiyoshi.yagi@riken.jp