Expected Preparations:

  Properties of atoms:
The periodic system; Covalent and non-covalent interactions; Naming molecules.
   Properties of molecules:
Molecular structure; The hydrophobic effect; Stereochemistry; Steric complementarity as the foundation of molecular function.
   Physical chemistry:
Kinetics, transition states, and equilibria; Enthalpy, entropy, and free energy; Boltzmann’s law.
   Biomolecules:
The molecules of life; The genetic code; Nucleic acids; Amino acids; Protein folding; Post-translational modifications and protein biochemistry; Membrane proteins; Biological function.
   [BIN-SX]
Chimera 		 
  If you are not already familiar with the prior knowledge listed above, you need to prepare yourself from other information sources.   The units listed above are part of this course and contain important preparatory material.  
Keywords: Forcefield principles and components; molecular mechanics; statistical pseudo-energies
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.

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.

Evaluation:

NA: This unit is not evaluated for course marks.

Contents

A brief introduction to molecular forcefields. NA

Task…

 

Further Reading

Salsbury, Alexa M and Justin A Lemkul. (2021). “Recent developments in empirical atomistic force fields for nucleic acids and applications to studies of folding and dynamics”. Current Opinion in Structural Biology 67:9–17 .
[PMID: 32950937] [DOI: 10.1016/j.sbi.2020.08.003]

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, Olgun and Alexander D MacKerell. (2008). “Comparison of protein force fields for molecular dynamics simulations”. Methods in Molecular Biology (Clifton, N.j.) 443:63–88 .
[PMID: 18446282] [DOI: 10.1007/978-1-59745-177-2_4]

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.

Questions, comments

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References

Page ID: BIN-SX-Molecular_forcefields

Author:
Boris Steipe ( <boris.steipe@utoronto.ca> )
Created:
2017-08-05
Last modified:
2022-09-14
Version:
1.1
Version History:
–  1.1 2020 Maintenance
–  1.0 First live version
–  0.1 First stub
Tagged with:
–  Unit
–  Live
–  Has lecture slides
–  Has further reading

 

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