https://shabirahmad427.github.io/skaf-lab/tag/molecular-dynamics/Molecular DynamicsHugo Blox Builder (https://hugoblox.com)en-usMon, 01 Jan 2024 00:00:00 +0000https://shabirahmad427.github.io/skaf-lab/media/icon_hu_16e4322de0c64ea4.pnghttps://shabirahmad427.github.io/skaf-lab/tag/molecular-dynamics/https://shabirahmad427.github.io/skaf-lab/project/molecular-dynamics/Mon, 01 Jan 2024 00:00:00 +0000https://shabirahmad427.github.io/skaf-lab/project/molecular-dynamics/<p>We develop and apply <strong>molecular dynamics (MD) simulations</strong> to investigate the structure, dynamics, and thermodynamics of complex molecular systems including proteins, enzymes, liquids, and nanomaterials.</p> <h2 id="methods">Methods</h2> <ul> <li>Classical and enhanced-sampling MD simulations</li> <li>Free energy calculations</li> <li>QM/MM approaches</li> <li>Development of force fields and simulation protocols</li> </ul> <h2 id="goals">Goals</h2> <ul> <li>Understand molecular recognition and binding</li> <li>Elucidate reaction mechanisms in enzymes</li> <li>Predict thermodynamic and transport properties of liquids</li> <li>Connect atomistic structure to macroscopic observables</li> </ul>