Biomolecular simulation: Difference between revisions
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== General == | == General == | ||
Biomolecular simulation<ref name="ARB_2012">Ron O. Dror, Robert M. Dirks, J.P. Grossman, Huafeng Xu, and David E. Shaw. "Biomolecular Simulation: A Computational Microscope for Molecular Biology." ''Annual Review of Biophysics'', 41:429-452, 2012. https://doi.org/10.1146/annurev-biophys-042910-155245</ref> is the application of molecular dynamics simulations to biochemical research questions. Processes that can be modeled include, but are not limited to, protein folding, drug binding, membrane transport, and the conformational changes critical to protein function. | |||
While biomolecular simulation could be considered a sub-field of computational chemistry, it is sufficiently specialized that Compute Canada has a Biomolecular Simulations National Team that supports this area. There is nevertheless some overlap of software tools between the two fields. See [[Computational chemistry]] for an annotated list of available software packages in that area. | |||
== Software Packages == | == Software Packages == | ||
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* [http://www.plumed-code.org PLUMED], a library for code development related to the calculation of free energy in molecular dynamics simulations. See also [[GROMACS]]. | * [http://www.plumed-code.org PLUMED], a library for code development related to the calculation of free energy in molecular dynamics simulations. See also [[GROMACS]]. | ||
* [https://www.rosettacommons.org Rosetta] | * [https://www.rosettacommons.org Rosetta] | ||
== References == | |||
Revision as of 17:46, 17 January 2018
This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.
General
Biomolecular simulation[1] is the application of molecular dynamics simulations to biochemical research questions. Processes that can be modeled include, but are not limited to, protein folding, drug binding, membrane transport, and the conformational changes critical to protein function.
While biomolecular simulation could be considered a sub-field of computational chemistry, it is sufficiently specialized that Compute Canada has a Biomolecular Simulations National Team that supports this area. There is nevertheless some overlap of software tools between the two fields. See Computational chemistry for an annotated list of available software packages in that area.
Software Packages
The following software packages are available on Compute Canada's HPC resources:
- GROMACS
- NAMD
- DL_POLY
- LAMMPS
- OpenKIM, the Knowledgebase of Interatomic Models
- OpenMM
- PLUMED, a library for code development related to the calculation of free energy in molecular dynamics simulations. See also GROMACS.
- Rosetta
References
- ↑ Ron O. Dror, Robert M. Dirks, J.P. Grossman, Huafeng Xu, and David E. Shaw. "Biomolecular Simulation: A Computational Microscope for Molecular Biology." Annual Review of Biophysics, 41:429-452, 2012. https://doi.org/10.1146/annurev-biophys-042910-155245