A top-down and bottom-up combined strategy for parameterization of coarse-grained force fields for phospholipids

Abstract

Coarse-graining (CG) molecular dynamics (MD) simulations are widely used in interpreting experimental observations and predicting assembly morphology as well as collective behaviour but also face the problem of poor accuracy....

Structural and thermodynamic properties of bulk triglycerides and triglyceride/water mixtures reproduced using a polarizable coarse-grained model

“…In the coarse-grained simulations, we employed a piecewise Morse function 42–46 to describe the nonbonded van der Waals interaction between two beads at a distance of r ij :Here, ε and R 0 represent the potential strength and equilibrated position of the function, respectively, while f is a step function that has a significant influence on the potential well shape. For two neutral particles, f is simply a constant, α or β , at distances less than R 0 or greater than R 0 , i.e.…”

“…In the coarse-grained simulations, we employed a piecewise Morse function [42][43][44][45][46] to describe the nonbonded van der Waals interaction between two beads at a distance of r ij :…”

“…Moreover, the extension of the local optimal path is promising to lead the parameters to an optimum without being trapped in a local extreme. [42][43][44][45][46] This method allows us to automatically optimize the FF of complex CG models with many interaction parameters, such as polarizable models.…”

“…A new set of CG FFs called the optimized morse force field (OMFF) has been constructed for (both nonpolarizable and polarizable) water, 42,43 alkanes, 43 alcohols, 44 and a dozen weakly polar molecules (or groups) 45 and applied to simulate polyethylene glycol aqueous solutions 42 and phospholipid assemblies. 46 In this work, we extend the OMFF to TGs based on a polarizable CG water (PCGW) model. This novel FF, called the polarizable optimized morse force field (p-OMFF), shows priority in simulating bulk TGs, TG/air interfaces, and TG/water mixtures compared to other CG methods.…”

Development of a bottom‐up coarse‐grained model for interactions of lipids with TiO 2 nanoparticles

“…46 There has been also a recent attempt to combine top-down and bottom-up approaches when parameterizing CG force fields for phospholipids. 47 Another recent work introduces a polarizable CG model for metal and metal oxide nanoparticles derived from ab initio data. 48,49 However, to our knowledge, the bottom-up approaches have not been used to parameterize interactions of nanomaterials and biomolecular systems, in particular, lipid membranes.…”