NAMD goes quantum: an integrative suite for hybrid simulations

Marcelo C R Melo1,2, Rafael C Bernardi1, Till Rudack1,3

  • 1NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.

Nature Methods
|March 27, 2018
PubMed
Summary

Hybrid quantum mechanics/molecular mechanics (QM/MM) methods enable reaction mechanism studies. The QwikMD suite integrates popular QM/MM software for streamlined setup, execution, and analysis of complex biological systems.

Related Concept Videos

Quantum Numbers02:43

Quantum Numbers

It is said that the energy of an electron in an atom is quantized; that is, it can be equal only to certain specific values and can jump from one energy level to another but not transition smoothly or stay between these levels.
52.3K
The Quantum-Mechanical Model of an Atom02:45

The Quantum-Mechanical Model of an Atom

Shortly after de Broglie published his ideas that the electron in a hydrogen atom could be better thought of as being a circular standing wave instead of a particle moving in quantized circular orbits, Erwin Schrödinger extended de Broglie’s work by deriving what is now known as the Schrödinger equation. When Schrödinger applied his equation to hydrogen-like atoms, he was able to reproduce Bohr’s expression for the energy and, thus, the Rydberg formula governing hydrogen spectra.
59.7K
Hybrid Zones02:29

Hybrid Zones

Hybrid zones are narrow regions where two closely related species interact, mate, and produce hybrids. Relative to either parent species, hybrids may possess distinct phenotypic or genetic differences that impact their survival and reproductive success. The genetic variances introduced by hybridization influence species diversity and speciation processes within the hybrid zone.
22.0K
Hybridization of Atomic Orbitals I03:24

Hybridization of Atomic Orbitals I

The mathematical expression known as the wave function, ψ, contains information about each orbital and the wavelike properties of electrons in an isolated atom. When atoms are bound together in a molecule, the wave functions combine to produce new mathematical descriptions that have different shapes. This process of combining the wave functions for atomic orbitals is called hybridization and is mathematically accomplished by the linear combination of atomic orbitals. The new orbitals that...
67.8K
Hybridization of Atomic Orbitals II03:35

Hybridization of Atomic Orbitals II

sp3d and sp3d 2 Hybridization
49.3K
Integration by Parts: Indefinite Integrals01:26

Integration by Parts: Indefinite Integrals

Integration by parts is a fundamental technique in calculus for evaluating integrals involving the product of two functions. It is particularly useful when direct integration is not feasible. The method is based on the product rule for differentiation, which states that the derivative of a product equals the derivative of the first function times the second, plus the first function times the derivative of the second. By integrating this identity and rearranging terms, the integration by parts...
230