Difference between revisions of "BIN-SX-Molecular forcefields"
Jump to navigation
Jump to search
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.
m |
m |
||
| (6 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | <div id=" | + | <div id="ABC"> |
| − | + | <div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;"> | |
Molecular Forcefields | Molecular Forcefields | ||
| − | + | <div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; "> | |
| − | + | (Principles and components - molecular mechanics, and statistical pseudo-energies.) | |
| − | + | </div> | |
| − | |||
| − | <div | ||
| − | |||
| − | Principles and components - molecular mechanics, and statistical pseudo-energies. | ||
</div> | </div> | ||
| − | {{ | + | {{Smallvspace}} |
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | <div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;"> | |
| − | + | <div style="font-size:118%;"> | |
| − | + | <b>Abstract:</b><br /> | |
| − | |||
| − | |||
| − | |||
| − | < | ||
| − | <div | ||
| − | |||
<section begin=abstract /> | <section begin=abstract /> | ||
| − | |||
A brief introduction to molecular forcefields. | A brief introduction to molecular forcefields. | ||
<section end=abstract /> | <section end=abstract /> | ||
| − | + | </div> | |
| − | + | <!-- ============================ --> | |
| − | + | <hr> | |
| − | + | <table> | |
| − | == | + | <tr> |
| − | === | + | <td style="padding:10px;"> |
| − | < | + | <b>Objectives:</b><br /> |
| − | <!-- | + | This unit will ... |
| − | 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: | + | * ... briefly introduce molecular mechanics and statistical forcefields. |
| − | < | + | </td> |
| − | + | <td style="padding:10px;"> | |
| + | <b>Outcomes:</b><br /> | ||
| + | After working through this unit you ... | ||
| + | * ... are familar with the components of a molecular mechanics forcefield, and how statistical forcefields are constructed. | ||
| + | </td> | ||
| + | </tr> | ||
| + | </table> | ||
| + | <!-- ============================ --> | ||
| + | <hr> | ||
| + | <b>Deliverables:</b><br /> | ||
| + | <section begin=deliverables /> | ||
| + | <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>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>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li> | ||
| + | <section end=deliverables /> | ||
| + | <!-- ============================ --> | ||
| + | <hr> | ||
| + | <section begin=prerequisites /> | ||
| + | <b>Prerequisites:</b><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 /> | ||
*<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; | ||
| − | |||
*<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. | ||
| − | |||
*<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. | ||
| − | + | This unit builds on material covered in the following prerequisite units:<br /> | |
| − | + | *[[BIN-SX-Chimera|BIN-SX-Chimera (UCSF ChimeraX: Structure Visualization and Analysis)]] | |
| − | *[[BIN-SX-Chimera|BIN-SX-Chimera (UCSF | + | <section end=prerequisites /> |
| − | + | <!-- ============================ --> | |
| − | + | </div> | |
| − | |||
| − | |||
| − | |||
| − | === | ||
| − | < | ||
| − | |||
| − | |||
| − | {{ | + | {{Smallvspace}} |
| − | |||
| − | |||
| − | |||
| − | |||
| − | {{ | + | {{Smallvspace}} |
| − | + | __TOC__ | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
{{Vspace}} | {{Vspace}} | ||
| Line 84: | Line 68: | ||
=== Evaluation === | === Evaluation === | ||
| − | |||
| − | |||
<b>Evaluation: NA</b><br /> | <b>Evaluation: NA</b><br /> | ||
| − | :This unit is not evaluated for course marks. | + | <div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div> |
| − | |||
| − | |||
| − | |||
| − | |||
| − | </div | ||
| − | |||
== Contents == | == Contents == | ||
| − | |||
{{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}}. | ||
| Line 102: | Line 77: | ||
{{Vspace}} | {{Vspace}} | ||
| − | |||
| − | |||
| − | |||
| − | |||
== Further reading, links and resources == | == Further reading, links and resources == | ||
| + | {{#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}} | ||
| − | |||
| − | |||
| − | |||
| − | |||
== Notes == | == Notes == | ||
| − | |||
| − | |||
<references /> | <references /> | ||
{{Vspace}} | {{Vspace}} | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
<div class="about"> | <div class="about"> | ||
| Line 170: | Line 96: | ||
:2017-08-05 | :2017-08-05 | ||
<b>Modified:</b><br /> | <b>Modified:</b><br /> | ||
| − | : | + | :2020-09-26 |
<b>Version:</b><br /> | <b>Version:</b><br /> | ||
| − | :1. | + | :1.1 |
<b>Version history:</b><br /> | <b>Version history:</b><br /> | ||
| + | *1.1 2020 Maintenance | ||
*1.0 First live version | *1.0 First live version | ||
*0.1 First stub | *0.1 First stub | ||
</div> | </div> | ||
| − | |||
| − | |||
{{CC-BY}} | {{CC-BY}} | ||
| + | [[Category:ABC-units]] | ||
| + | {{UNIT}} | ||
| + | {{LIVE}} | ||
</div> | </div> | ||
<!-- [END] --> | <!-- [END] --> | ||
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:
|
Outcomes:
|
Deliverables:
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:
- 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 ] 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 ] 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
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.
