Titlebook: Computer Simulations in Molecular Biology; Hiqmet Kamberaj Textbook 2023 The Editor(s) (if applicable) and The Author(s), under exclusive

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Equilibration of a Molecular Biological System Simulation,This chapter introduces the setup protocol for preparing a molecular biological system simulation in explicit solvent. The energy minimisation methods are discussed in details. Furthermore, the complete protocol of the equilibration of solvent is shown for a protein system in explicit solvent.

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Normal Mode Analysis,This chapter introduces the normal mode analysis of a protein, which is associated with the energy minimisation.

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https://doi.org/10.1007/978-3-031-34839-6Quantum Mechanics Simulations; Coarse-Grained Models; Semi-Empirical Models; Software Trends; Molecular

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Computer Simulations in Molecular Biology978-3-031-34839-6Series ISSN 1434-8322 Series E-ISSN 2198-2589

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