Development of Coarse‐Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm

Abstract

A fast, reasonable, and transferable coarse-grained (CG) molecular dynamics force field (FF) is essential to combine experimental and simulation data. However, the parameterization of CG FF usually requires massive computation, which hinders its rapid development. Here, we presented an efficient optimization protocol by combining multilinear interpolation technique with simplex algorithm. In this preliminary work, taking the experimental properties as the benchmark, we constructed a new set of CG FF for water and n-alkanes by adopting piecewise Morse function to describe the nonbonded interactions. This CG FF has a delicate balance between efficiency, accuracy, and transferability and well reproduced the correct structural and thermodynamics properties of pure water and alkane liquids. More importantly, optimized Morse potential was also successfully applied to describe the interactions between water and n-alkanes. It nicely predicted the phase separation, interface tension, hydration free energy, and formation of microemulsions of water/oil mixtures.

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

“…Nonbonded interactions are excluded for beads separated by one bond to avoid offset in L b . 35 Dihedral interactions in hydrocarbons and lipids are not introduced in the present work. We found that the inclusion of dihedral only improved the agreement of dihedral angle distributions with AA MD but had little impact on the thermodynamic properties and raised additional computation cost instead.…”

“…The computational details can be found in our previous work. 35 Properties of membranes. Both the structure and thermodynamic properties of dimyristoyl phosphatidylcholine (DMPC) and dipalmitoyl phosphatidylcholine (DPPC) membranes were evaluated using OPT1.35 FF.…”

Is an Inductive Effect Explicit Account Required for Atomic Charges Aimed at Use within the Force Fields?

“…A local optimization was produced using the Nelder–Mead (simplex) algorithm, which is shown to be successfully applied for force field parameterization. − Due to its stochastic nature, in contrast to gradient methods, it tends to be much less affected by low curvature of the cost function along with the “loose” degenerate collective modes, which would naturally occur in such a task. , Additionally, the final parameters obtained from several runs help to estimate the parameter dispersion and hence the degeneracy of the cost function with respect to collective modes, containing certain atomic parameters.…”

Empirical quality criteria for the approximation of the electronic term of a diatomic molecule by the Morse formula

“…The Morse model potential [1], despite a very rough approximation, is widely used in molecular spectroscopy and in other areas of optics and chemical physics. According to the Chemical Abstracts Service, over 6,000 references are given on the request " Morse Formula" Ȧs an example, we present random selections of recent studies in the field of spectroscopy [2][3][4][5][6][7][8][9][10][11][12][13], the influence of an external field, laser dissociation of moleculescool [14][15][16][17][18][19][20][21][22][23][24], thermodynamics, kinetics [25][26][27][28][29][30][31][32][33][34], solid and liquid physicssti [35][36][37][38][39][40][41][42][43][44], intermolecular interactions [45][46][47]…”