BIN-SX-Molecular forcefields

Molecular Forcefields

(Principles and components - molecular mechanics, and statistical pseudo-energies.)

 

Abstract:

A brief introduction to molecular forcefields.

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Objectives: This unit will ... ... briefly introduce molecular mechanics and statistical forcefields.

Outcomes: After working through this unit you ... ... are familar with the components of a molecular mechanics forcefield, and how statistical forcefields are constructed.

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Deliverables:

Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.

Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.

Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

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Prerequisites:
You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:

• Properties of atoms: the periodic system, covalent and non-covalent interactions; naming atoms and molecules;
• Properties of molecules: molecular structure, the hydrophobic effect; stereochemistry; steric complementarity as the foundation of molecular function.
• Physical chemistry: Kinetics and equilibria, transition states, chemical reactions; enthalpy, entropy and free energy; acid-base equilibria, Boltzmann's law.

This unit builds on material covered in the following prerequisite units:

• BIN-SX-Chimera (UCSF ChimeraX: Structure Visualization and Analysis)

 

 

 

Evaluation

Evaluation: NA

This unit is not evaluated for course marks.

Contents

Task:

• Read the introductory notes on forcefields for macromolecular structure analysis.

 

Further reading, links and resources

Salsbury & Lemkul (2020) Recent developments in empirical atomistic force fields for nucleic acids and applications to studies of folding and dynamics. Curr Opin Struct Biol 67:9-17. (pmid: 32950937)

[ PubMed ] [ DOI ] Abstract Nucleic acids play critical roles in carrying genetic information, participating in catalysis, and preserving chromosomal structure. Despite over a century of study, efforts to understand the dynamics and structure-function relationships of DNA and RNA at the atomic level are still ongoing. Molecular dynamics (MD) simulations augment experiments by providing atomistic resolution and quantitative relationships between structure and conformational energy. Steady advancements in computer hardware, software, and atomistic force fields (FFs) over 40 years have facilitated new discoveries. Here, we review nucleic acid FF development with emphasis on recent refinements that have improved descriptions of important nucleic acid properties. We then discuss several key examples of successes and challenges in modeling nucleic acid structure and dynamics using the latest FFs.

Force Fields for MD simulations a concise but comprehensive slide-deck from the UIUC Computational Biophysics Workshop, San Francisco 2005. (Author probably Emad Tajkhorshid)

Guvench & MacKerell (2008) Comparison of protein force fields for molecular dynamics simulations. Methods Mol Biol 443:63-88. (pmid: 18446282)

[ PubMed ] [ DOI ] Abstract In the context of molecular dynamics simulations of proteins, the term "force field" refers to the combination of a mathematical formula and associated parameters that are used to describe the energy of the protein as a function of its atomic coordinates. In this review, we describe the functional forms and parameterization protocols of the widely used biomolecular force fields Amber, CHARMM, GROMOS, and OPLS-AA. We also summarize the ability of various readily available noncommercial molecular dynamics packages to perform simulations using these force fields, as well as to use modern methods for the generation of constant-temperature, constant-pressure ensembles and to treat long-range interactions. Finally, we finish with a discussion of the ability of these force fields to support the modeling of proteins in conjunction with nucleic acids, lipids, carbohydrates, and/or small molecules.

Notes

 

About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2020-09-26

Version:

1.1

Version history:

• 1.1 2020 Maintenance
• 1.0 First live version
• 0.1 First stub

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