Computational chemistry: Difference between revisions
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*[https://en.wikipedia.org/wiki/Molecular_mechanics Molecular mechanics] methods, based on classical mechanics instead of quantum mechanics, are yet faster but yet more narrowly applicable. They are nevertheless extremely useful in the study of biological systems. | *[https://en.wikipedia.org/wiki/Molecular_mechanics Molecular mechanics] methods, based on classical mechanics instead of quantum mechanics, are yet faster but yet more narrowly applicable. They are nevertheless extremely useful in the study of biological systems. | ||
<!--T: | === Notes on installed software === <!--T:4--> | ||
Following is a survey of the resources available for high-accuracy computational chemistry. Bear in mind however that the distinction is artificial and many tools are applicable to both biological and non-biological systems. | |||
==== Applications ==== <!--T:5--> | ==== Applications ==== <!--T:5--> | ||
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* [http://departments.icmab.es/leem/siesta SIESTA] | * [http://departments.icmab.es/leem/siesta SIESTA] | ||
* [[VASP]] | * [[VASP]] | ||
* See the [[Biomolecular simulation]] page for a discussion on the resources relevant to this area of research. | |||
The automatically generated list of versions installed on Compute Canada systems can be found in [[Available software]]. | The automatically generated list of versions installed on Compute Canada systems can be found in [[Available software]]. | ||
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* [http://openbabel.org OpenBabel], a set of tools to enable one "to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas." | * [http://openbabel.org OpenBabel], a set of tools to enable one "to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas." | ||
* [https://pcmsolver.readthedocs.org PCMSolver], a tool for code development related to the Polarizable Continuum Model. (Some applications listed above offer built-in capabilities related to the PCM.) | * [https://pcmsolver.readthedocs.org PCMSolver], a tool for code development related to the Polarizable Continuum Model. (Some applications listed above offer built-in capabilities related to the PCM.) | ||
* [https://github.com/atztogo/spglib Spglib], a code library for development relating to | * [https://github.com/atztogo/spglib Spglib], a code library for development relating to the symmetry of crystals. | ||
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Revision as of 21:58, 17 January 2018
Computational chemistry is a branch of chemistry that incorporates the results of theoretical chemistry into computer programs to calculate the structures and properties of molecules and solids.
Computational chemistry methods range from highly accurate to very approximate.
- Ab initio methods, based entirely on first principles, tend to be broadly applicable but very costly.
- Semi-empirical methods give accurate results for a narrower range of cases, but are also typically much faster than ab initio methods.
- Density functional methods may be thought of as a compromise in cost between ab initio and semi-empirical methods.
- Molecular mechanics methods, based on classical mechanics instead of quantum mechanics, are yet faster but yet more narrowly applicable. They are nevertheless extremely useful in the study of biological systems.
Notes on installed software
Following is a survey of the resources available for high-accuracy computational chemistry. Bear in mind however that the distinction is artificial and many tools are applicable to both biological and non-biological systems.
Applications
Follow the link to read about the capabilities of any of the following packages:
- Abinit
- CP2K
- CPMD
- deMon
- GAMESS-US
- Gaussian (on Graham only)
- NWChem
- ORCA
- PSI4
- Quantum ESPRESSO
- SIESTA
- VASP
- See the Biomolecular simulation page for a discussion on the resources relevant to this area of research.
The automatically generated list of versions installed on Compute Canada systems can be found in Available software.
Libraries and tools
- CheMPS2, a "library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry."
- Libxc, a code library of density-functional models.
- Molden, a visualization tool for use in conjunction with GAMESS, Gaussian, & others.
- Open3DQSAR, a "tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields."
- OpenBabel, a set of tools to enable one "to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas."
- PCMSolver, a tool for code development related to the Polarizable Continuum Model. (Some applications listed above offer built-in capabilities related to the PCM.)
- Spglib, a code library for development relating to the symmetry of crystals.