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Ever wondered which molecular forcefield you should use for MD simulations of lipid membranes? The three most popular all-atom parameter sets, AMBER Lipid21, CHARMM36, and Slipids-2020 are quite similar in equilibrium properties. But what about under deformation? www.biorxiv.org/content/10.6...

biorxiv.orgChoosing a lipid force field for membrane remodeling: pore formation and membrane mimetics in CHARMM36, AMBER Lipid21 and SlipidsMolecular dynamics simulations have been used to study how proteins or nucleic acids interact with lipid membranes. Such simulations often face a compromise, because state-of-the art performance on sp...

Erik Poppleton

@poppleton.phd

Pore formation and lipid rearrangement are important features of lipid membranes, important for understanding the fundamental biology of cells and the mechanics of electroporation and membrane-active molecules in synthetic biology applications.

27/10/26, 12:58 pm0 reposts0 likes

Erik Poppleton

@poppleton.phd

This project was inspired by noticing that the Chain Coordinate for pore formation gave very different results if you used Lipid21 compared with CHARMM36 to form pores in DMPC membranes. Turns out the three behave quite differently when you start deforming the membranes.

Erik Poppleton

@poppleton.phd

Pore formation energy barriers computed using the three force fields for different lipids revealed a consistent pattern. Lipid21 had a higher energy barrier than the other two. This appears to correlate with tilt modulus (k_θ) - how easy it is to rotate a lipid against the membrane normal.

Erik Poppleton

@poppleton.phd

Further, these pores had very short lifetimes when the biasing potential was dropped. It should be noted, however, that experimental measurements of pore lifetimes under electrical potentials give much longer lifetimes than observed in MD simulations.

Erik Poppleton

@poppleton.phd

Morphology of formed pores followed from the observed energy barriers and metastability. CHARMM36 and Slipids rearranged into toroidal pores, while Lipid21 had a core composed of pure water and resisted formation the entire way.