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Computational chemistry: Difference between revisions
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Most computer programs in the field offer a large number of methods, each method with its own accuracy, range of applicability, and computational cost. The methods can be broadly grouped together in terms of the trade-off between accuracy, applicability, and cost. | |||
*[https://en.wikipedia.org/wiki/Ab_initio_quantum_chemistry_methods '' | *[https://en.wikipedia.org/wiki/Ab_initio_quantum_chemistry_methods ''ab initio''] methods, based entirely on first principles, tend to be broadly applicable but very costly in terms of CPU time; they are therefore mostly applied to systems with a small number of particules. | ||
*[https://en.wikipedia.org/wiki/Semi-empirical_quantum_chemistry_method Semi-empirical] methods give accurate results for a narrower range of cases, but are also typically much faster than ''ab initio'' methods. | *[https://en.wikipedia.org/wiki/Semi-empirical_quantum_chemistry_method Semi-empirical] methods give accurate results for a narrower range of cases, but are also typically much faster than ''ab initio'' methods. | ||
*[https://en.wikipedia.org/wiki/Density_functional_theory Density functional] methods may be thought of as a compromise in cost between ''ab initio'' and semi-empirical methods. | *[https://en.wikipedia.org/wiki/Density_functional_theory Density functional] methods may be thought of as a compromise in cost between ''ab initio'' and semi-empirical methods. The cost-accuracy trade-off is very good and density functional methods have therefore become very widely used in recent years. | ||
*[https://en.wikipedia.org/wiki/Molecular_mechanics Molecular mechanics] methods, based on classical mechanics instead of quantum mechanics, are | |||
*[https://en.wikipedia.org/wiki/Molecular_mechanics Molecular mechanics] methods, based on classical mechanics instead of quantum mechanics, are faster but more narrowly applicable. They use a force field that can be optimized using ''ab initio'' and/or experimental data to reproduce the properties of the materials. Because of the low cost, molecular mechanics methods are frequently used for molecular dynamics calculations and can be applied to systems of thousands or even millions of particles. | |||
Molecular dynamics calculations are extremely useful in the study of biological systems. Please see the [[Biomolecular simulation]] page for a list of the resources relevant to this area of research, but bear in mind that the distinction is artificial and many tools are applicable to both biological and non-biological systems. They can be used to simulate glasses, metals, liquids, supercooled liquids, granular materials, complex materials, etc. | |||
=== Notes on installed software === <!--T:4--> | === Notes on installed software === <!--T:4--> | ||
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* [http://cpmd.org CPMD] | * [http://cpmd.org CPMD] | ||
* [http://www.demon-software.com/public_html/program.html deMon] | * [http://www.demon-software.com/public_html/program.html deMon] | ||
* DL-POLY | |||
* [http://www.msg.chem.iastate.edu/gamess/index.html GAMESS-US] | * [http://www.msg.chem.iastate.edu/gamess/index.html GAMESS-US] | ||
* [[Gaussian]] | * [[Gaussian]] | ||
* GROMACS | |||
* LAMMPS | |||
* NAMD | |||
* [http://www.nwchem-sw.org NWChem] | * [http://www.nwchem-sw.org NWChem] | ||
* [[ORCA]] | * [[ORCA]] | ||
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An automatically generated list of versions installed on Compute Canada systems can be found on [[Available software]]. | An automatically generated list of all the versions installed on Compute Canada systems can be found on [[Available software]]. | ||
====Visualization tools==== | |||
Molden, a visualization tool for use in conjunction with GAMESS, Gaussian and other applications. | |||
VMD, an open-source molecular visualization program for displaying, animating, and analyzing large biomolecular systems in 3D | |||
VisIt is a general-purpose 3D visualization tool, but the gallery includes examples from chemistry | |||
See Visualization for more about producing visualizations on Compute Canada clusters. | |||
==== Libraries and tools ==== <!--T:7--> | ==== Libraries and tools ==== <!--T:7--> | ||
* [https://github.com/SebWouters/CheMPS2 CheMPS2], a "library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry." | * [https://github.com/SebWouters/CheMPS2 CheMPS2], a "library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry." | ||
* [http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Libxc], a | * [http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Libxc], a library of density-functional models. | ||
* [http://www.cmbi.ru.nl/molden/ Molden], a visualization tool for use in conjunction with GAMESS, Gaussian, & others. | * [http://www.cmbi.ru.nl/molden/ Molden], a visualization tool for use in conjunction with GAMESS, Gaussian, & others. | ||
* [http://open3dqsar.sourceforge.net/?Home Open3DQSAR], a "tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields." | * [http://open3dqsar.sourceforge.net/?Home Open3DQSAR], a "tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields." | ||
* [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. | * [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 | * [https://github.com/atztogo/spglib Spglib], a library for development relating to the symmetry of crystals. | ||
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