Molecular Simulations Guidelines for Biological Nanomaterials: From Peptides to Membranes

Irene Marzuoli; Franca Fraternali

doi:10.1007/978-1-0716-0928-6_6

Molecular Simulations Guidelines for Biological Nanomaterials: From Peptides to Membranes

Irene Marzuoli, Franca Fraternali

GSTT Guy's and St Thomas' NHS Foundation Trust

Research output: Contribution to journal › Article › peer-review

Abstract

In studying biological processes and focusing on the molecular mechanisms at the basis of these, molecular dynamics (MD) simulations have demonstrated to be a very useful tool for the past 50 years. This suite of computational methods calculates the time-dependent evolution of a molecular system using physics-based first principles. In this chapter, we give a brief introduction to the theory and practical use of molecular dynamics simulations, highlighting the different models and algorithms that have been developed to tackle specific problems, with a special focus on classical force fields. Some examples of how simulations have been used in the past will help the reader in discerning their power, limitations, and significance.

Original language	English
Pages (from-to)	81-100
Number of pages	20
Journal	Methods in molecular biology (Clifton, N.J.)
Volume	2208
DOIs	https://doi.org/10.1007/978-1-0716-0928-6_6
Publication status	Published - 1 Jan 2021

Keywords

Coarse-grained parametrization
Force fields
Lipids
Molecular dynamics
Multiscale modeling
Proteins
Simulations

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10.1007/978-1-0716-0928-6_6

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abstract = "In studying biological processes and focusing on the molecular mechanisms at the basis of these, molecular dynamics (MD) simulations have demonstrated to be a very useful tool for the past 50 years. This suite of computational methods calculates the time-dependent evolution of a molecular system using physics-based first principles. In this chapter, we give a brief introduction to the theory and practical use of molecular dynamics simulations, highlighting the different models and algorithms that have been developed to tackle specific problems, with a special focus on classical force fields. Some examples of how simulations have been used in the past will help the reader in discerning their power, limitations, and significance.",

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Molecular Simulations Guidelines for Biological Nanomaterials: From Peptides to Membranes

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Keywords

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