CrunchYard has spent over a decade applying high performance computing capabilities to a wide range of scenarios, problems and use cases. Our payoff line says we offer the POWER TO SIMULATE – ANYTHING – and we mean it. Some of the biggest challenges of our age can be solved quicker and better through the use of true HPC capabilities. In this blog, we look at HPC applications in Computational Chemistry.

 Computational chemistry is a branch of chemistry that uses computer simulations to assist in solving chemical problems – which is to say, nearly any chemistry or chemical projects might use computational modelling.

 The Nobel Prize in Chemistry for 2013 was awarded jointly to Martin Karplus, Michael Levitt, and Arieh Warshel for their work on the development of multiscale models for complex chemical systems.

 Their research pioneered the use of computer simulations to understand and predict chemical processes, bridging the gap between classical physics and quantum chemistry. The impact of this work is profound, as it transformed theoretical chemistry from a field that relied heavily on abstract theories into one that uses powerful computational tools to solve real-world problems.

 The ability to simulate chemical processes accurately has become a fundamental part of modern chemistry, influencing numerous areas including medicine, materials science, and environmental science. From new pharmaceutical models to better biofuels, better soles for sneakers to new fire-resistant coatings… chemistry can be found in nearly every new innovation and is fantastically broad in its application as a field.

 An example in practice

Consider the example of an enzyme-catalyzed reaction. Enzymes are large biological molecules that facilitate chemical reactions. To understand how an enzyme works, scientists need to know how the reactants interact with the enzyme at the molecular level. Using the multiscale models developed by Karplus, Levitt, and Warshel, researchers can simulate the entire reaction process. The quantum mechanics part of the simulation models the electronic changes during the reaction, while the classical mechanics part handles the larger-scale movements of the enzyme and surrounding molecules.

See computational chemistry in action for yourself in this clip on YouTube, demonstrating another example:

CrunchYard supports a wide range of computational chemistry applications and software programmes and have extensive experience implementing turnkey and bespoke HPC systems for Computational Chemistry applications. Below is a sampling of some of the open source and license-codes we have worked with, enabling small and large teams of computational chemists to create extraordinary solutions for a world hungry for innovation. It isn’t an exhaustive list, but covers the most commonly used codes in the wide range of applications chemistry has in practice.

• GROMACS - Molecular dynamics simulations.
• LAMMPS - Classical molecular dynamics for materials modelling.
• Quantum ESPRESSO - Electronic-structure calculations and materials modelling.
• NWChem - Large-scale computational chemistry problems.
• CP2K - Atomistic and molecular simulations for various systems.
• OpenMM - Molecular simulation toolkit.
• ORCA - Molecular properties with quantum chemical methods.
• Psi4 - Quantum mechanical behaviour of molecules.
• Q-Chem - Ab initio quantum chemistry.
• DALTON - Molecular electronic structure calculations.
• PySCF - Electronic structure platform in Python.
• GAMESS (US) - Ab initio quantum chemistry calculations.
• ABINIT - Properties of systems using DFT and perturbation theory.
• Octopus - Ab initio virtual experimentation.
• ERKALE - Molecular properties with Hartree–Fock and DFT.
• NAMD - Molecular dynamics for large biomolecular systems.
• Avogadro - Molecular editor and visualization tool.
• TINKER - Molecular mechanics and dynamics.
• ChemShell - Combines quantum chemistry and molecular mechanics.
• AmberTools - Molecular dynamics simulations.
• CPMD - Ab initio molecular dynamics.
• ADF - Density functional methods (partially open-source).