{"query": "Why do we get different parameter sets when looking at how ion and water-oxygen atoms interact?", "pos": "the problem here is which one to chose to obtain a consistent set of parameters. the multiple parameter sets arise because similar aij and bij terms can be obtained between the ion and water-oxygen atoms : for a certain rmin/2 and , there will be a corresponding bigger rmin/2 and smaller , or a smaller rmin/2 and bigger , which yield similar aij and bij terms (see eqs 54 and 55). when two different ion parameter sets, which give similar aij terms between an ion and oxygen in water, are applied to the same biomolecule, they may give quite different aij terms between the same atom type on the biomolecule and the metal ion after applying the combining rules."}
{"query": "Chemical physicists managed to mock-up ions in common force fields using the 12-6 Lennard-Jones model without any direct bonding, which verified the structure traits of water-based potassium.", "pos": "the 12-6 lj nonbonded model remains a fast and practical way to simulate ions using classical force fields. the blyp functional was used for the system containing a k ion and 59 water molecules. in total, 0.168 ps of equilibration and 1.98 ps of sampling were performed in the nve ensemble. good agreement between the cpmd and classical md simulations was obtained for the structural properties of aqueous k, validating in part the classical representation of the k ion. moreover, it has also shown that it is possible to simultaneously simulate two or more experimental properties for some of the monovalent ions (e.g., na, k, rb, cs) using the 12-6 lj nonbonded model."}
{"query": "Which concepts are encapsulated within classical models in AMOEBA?", "pos": "they also proposed that the ct effect may need to be included to improve the model. ponder, ren, and co-workers have created the atomic multipole optimized energetics for biomolecular simulation (amoeba) force field. it has bonded terms (bond, angle, dihedral, and improper torsion terms) represented using classical models. the bond and angle parameters are fit on the basis of qm-derived values (e.g., geometries and vibrational frequencies). the electrostatic interaction is represented by permanent monopoles (point charges), dipoles, and quadrupoles derived from the distributed multipole analysis (dma) procedure, along with the polarizable dipoles."}
