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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Sectionally Complemented LatticesThis chapter introduces the normal mode analysis of a protein, which is associated with the energy minimisation.

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The Congruences of a Finite LatticeThis chapter describes how to run standard MD simulations of a biological system in explicit solvent using different statistical ensembles and numerical integrators.

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The Congruences of a Finite LatticeThis chapter describes the principal components analysis of biological systems in explicit solvent and the stability of the principal components analysis by comparing the quasi-harmonic modes of different simulation trajectories of the same system.

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Quantum Mechanics Computer Simulations,In this chapter, we introduce the quantum mechanics molecular models and quantum mechanics molecular dynamics simulations of molecules and biomolecular systems. Besides, the numerical aspects of the non-relativistic electronic structure of molecular systems will be discussed.

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Basis Set Functions,In this chapter, we discuss the basis set functions for standard molecular quantum mechanics calculations. Furthermore, the basis sets for quantum periodic systems, such as solids and metals, will be described.

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Semi-empirical Quantum Mechanics Computer Simulations,In this chapter, we focus on the semi-empirical quantum mechanics approaches and their use in computer simulations.

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Machine Learning Quantum Mechanics Computer Simulations,This chapter introduces the machine learning quantum mechanics methods and their use in computer simulations. In particular, the focus is on the use of machine learning approach in predicting the potential electronic energy surface and its gradient for QM molecular dynamics simulations.

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Coarse-Grain Modelling Strategies,In this chapter, the computational coarse-grain modelling strategies are discussed. Besides, different coarse-grained models (CGMs) will be described.

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,Implementation of Molecular Dynamics in Simulations,In this chapter, we will briefly describe the practical aspects of molecular dynamics simulations, such as designing the constraints, periodic boundary conditions, spherical cutoffs, treatment of the long-range interactions (in particular, electrostatic interactions), and identifying the equilibrium states of the simulations.

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Python Interactive GUI for CHARMM Software Package,In this chapter, we will briefly describe a Python interactive graphical user interface (GUI) for CHARMM package for performing MD simulations of a biological molecular system and standard analysis of . data produced from the simulations.