Highlights of our Work
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Quantum mechanics (QM) is crucial to investigate subatomic mechanisms that occur in biology. However, studying entire biomolecular systems quantum mechanically is computationally prohibitive. Traditionally, NAMD employs classical molecular mechanics (MM) to determine the movement of a molecule, solving Newton's equations of motion and treating atoms as spheres and bonds as springs. Combining both approaches, hybrid QM/MM methods employ the quantum mechanics formalism to key regions of the biological system, while using molecular mechanics approach to include the effects of the surrounding area. NAMD's new QM/MM interface can be combined with many molecular dynamics protocols, such as enhanced sampling and free energy calculations. This combination was crucial in the investigation, appearing in Nature Methods, of the mechanism that sets the genetic code, when DNA's three-letter code is translated to protein's amino acid residues. Uniting a large set of tools in VMD, QwikMD, and NAMD, the QM/MM simulations revealed the subatomic details of this mechanism, providing an unique view for this essential step of life. Read more in Nature Methods, or from our QM/MM website.