Difference between revisions of "BIN-SX-Molecular forcefields"

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Molecular Forcefields
 
Molecular Forcefields
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(Principles and components - molecular mechanics, and statistical pseudo-energies.)
 
(Principles and components - molecular mechanics, and statistical pseudo-energies.)
 
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<b>Abstract:</b><br />
 
<b>Abstract:</b><br />
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<b>Deliverables:</b><br />
 
<b>Deliverables:</b><br />
 
<section begin=deliverables />
 
<section begin=deliverables />
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<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-time_management" -->
 
 
<li><b>Time management</b>: 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.</li>
 
<li><b>Time management</b>: 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.</li>
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<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-journal" -->
 
 
<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
 
<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
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<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" -->
 
 
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
 
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
 
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<section begin=prerequisites />
 
<section begin=prerequisites />
 
<b>Prerequisites:</b><br />
 
<b>Prerequisites:</b><br />
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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:<br />
 
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:<br />
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<!-- included from "./data/ABC-unit_prerequisites.txt", section: "che" -->
 
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<!-- included from "./data/ABC-unit_prerequisites.txt", section: "atoms" -->
 
 
*<b>Properties of atoms</b>: the periodic system, covalent and non-covalent interactions; naming atoms and molecules;
 
*<b>Properties of atoms</b>: the periodic system, covalent and non-covalent interactions; naming atoms and molecules;
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<!-- included from "./data/ABC-unit_prerequisites.txt", section: "molecules" -->
 
 
*<b>Properties of molecules</b>: molecular structure, the hydrophobic effect; stereochemistry; steric complementarity as the foundation of molecular function.
 
*<b>Properties of molecules</b>: molecular structure, the hydrophobic effect; stereochemistry; steric complementarity as the foundation of molecular function.
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<!-- included from "./data/ABC-unit_prerequisites.txt", section: "physchem" -->
 
 
*<b>Physical chemistry</b>: Kinetics and equilibria, transition states, chemical reactions; enthalpy, entropy and free energy; acid-base equilibria, Boltzmann's law.
 
*<b>Physical chemistry</b>: Kinetics and equilibria, transition states, chemical reactions; enthalpy, entropy and free energy; acid-base equilibria, Boltzmann's law.
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<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
 
 
This unit builds on material covered in the following prerequisite units:<br />
 
This unit builds on material covered in the following prerequisite units:<br />
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*[[BIN-SX-Chimera|BIN-SX-Chimera (UCSF Chimera: Structure Visualization and Analysis)]]
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*[[BIN-SX-Chimera|BIN-SX-Chimera (UCSF ChimeraX: Structure Visualization and Analysis)]]
 
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<section end=prerequisites />
 
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=== Evaluation ===
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<b>Evaluation: NA</b><br />
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
 
== Contents ==
 
== Contents ==
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{{Task|1=
 
{{Task|1=
 
*Read the introductory notes on {{ABC-PDF|BIN-SX-Molecular_forcefields|forcefields for macromolecular structure analysis}}.
 
*Read the introductory notes on {{ABC-PDF|BIN-SX-Molecular_forcefields|forcefields for macromolecular structure analysis}}.
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== Self-evaluation ==
 
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== Notes ==
 
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<references />
 
 
== Further reading, links and resources ==
 
== Further reading, links and resources ==
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{{#pmid: 32950937}}
 
<div class="reference-box">[http://www.ks.uiuc.edu/Training/Workshop/SanFrancisco/lectures/Wednesday-ForceFields.pdf '''Force Fields for MD simulations'''] a concise but comprehensive slide-deck from the [http://www.ks.uiuc.edu/Training/Workshop/SanFrancisco/ UIUC Computational Biophysics Workshop, San Francisco 2005]. (Author probably Emad Tajkhorshid)</div>
 
<div class="reference-box">[http://www.ks.uiuc.edu/Training/Workshop/SanFrancisco/lectures/Wednesday-ForceFields.pdf '''Force Fields for MD simulations'''] a concise but comprehensive slide-deck from the [http://www.ks.uiuc.edu/Training/Workshop/SanFrancisco/ UIUC Computational Biophysics Workshop, San Francisco 2005]. (Author probably Emad Tajkhorshid)</div>
 
{{#pmid: 18446282}}
 
{{#pmid: 18446282}}
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== Notes ==
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<references />
  
 
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<b>If in doubt, ask!</b> If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
 
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
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:2017-10-29
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:2020-09-26
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:1.0
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:1.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
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*1.1 2020 Maintenance
 
*1.0 First live version
 
*1.0 First live version
 
*0.1 First stub
 
*0.1 First stub
 
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Latest revision as of 11:44, 28 September 2020

Molecular Forcefields

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


 


Abstract:

A brief introduction to molecular forcefields.

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.

    • 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:


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    Task:


     

    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 ]

    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 ]

    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

    CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

    Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BIN-SX-Molecular_forcefields&oldid=11791"